I have tried to print Baby Groot , but every time I print the head, there are always layer shifts like the photos below. I have printed three heads and the layer shifts happened all in the same place.
I tried to print something else that is the (more or less) same height and the layer shifting also happened.
I was thinking maybe because z-rod bent. But apparently the layer shift happened in different height.
What is my problem and how to solve this ? I am using Ender 3 with BLTouch.
Layer shifting has two basic causes: the partially printed part moves or flexes, or the bed or Y carriage (almost always -- they seem rather uncommon on the X axis) skips one or more steps in one direction or the other.
Permanent layer shifts -- that is, where the entire print above the shift is and remains shifted -- are more likely to be the latter; temporary shifts (where the shift creates a bulge or groove, and then layers above that section are back in line with those below) are more likely due to part movement.
In your case, you appear to have temporary shifts. Those on the Groot head seem (in the photos) to line up with heights at which some of the peaks on the head end; they might be a result of changes in the nozzle interaction with a print that's becoming tall enough to flex as the path changes due to those sections finishing. The ones on the pink block look more like temporary overextrusion, but since we can't see the opposite side of whatever that is, I can't say for certain that they aren't the same thing.
One thing you might try is reslicing both of those objects with Z-hop enabled. That will reduce nozzle dragging over earlier parts of the current layer, which can flex the part (or temporarily block the nozzle, causing pressure buildup that will lead to momentary overextrusion).
To save time, you might look for whether you have any objects that exhibit this without as many hours of printing time (and tens of grams of filament) already spent -- perhaps you can sink Groot into the virtual bed in your slicer, so as to print him only from the eyes up (or even higher) -- though that might reduce flex enough that finishing the peaks on his head won't result in a significant change.
Zeiss Ikon's answer is good - but just in case that doesn't solve it, have you printed larger / longer prints before? There's a well known problem with the Ender 3's 4.2.2 motherboard that causes layer shifts as it overheats on longer prints. You can try elevating the printer and putting a fan underneath to see if that changes anything. (I had that problem and it drove me nuts until I got a 4.2.7 motherboard)
However, I do see some other layer issues on the head further down the print. I would probably loosen and readjust all the gantries again, check all the belt tensions, do another bed level (you changed out the stock springs with the yellow ones right?). After hours of use, not uncommon for there to be a hiccup, maybe a piece of plastic / dust stuck in a track.
If you've double checked and adjusted all the gantry's and none are loose or too tight, look at your table the printer sits on. If possible, put the printer on something really heavy (slab of concrete, thick wood) with a little padding underneath that heavy surface. Put a half glass of water on the top most surface (not on the printer) to see if the table is vibrating while printing (water should be still the entire time). It could be the table is moving a little as the printer is printing - with fractions of mm's it doesn't take too much.
These are (at least almost certainly) not layer shifts. A layer shift is when the physical toolhead position becomes inconsistent with the logical one because a stepper motor missed a step or the bed surface shifted or something else went wrong. It's possible for them to reverse if the same happens in the opposite direction at a later layer, but very unlikely.
What you have seems to be geometry-dependent inconsistent extrusion. If you look at the slicer output in an analyzer, you probably have some geometry difference in terms of number of components, travel moves needed, etc. at the affected layers, causing more or less material to be oozed/lost in the model's interior, thereby producing more of less extrusion thickness in the walls that follow, relative to other layers.
While there are probably other ways to reduce the impact, the right way to fix this is find the cause of the oozing and stop it. It's almost surely unretracted travel moves inside the model interior, which Cura calls "combing"; I don't know the Prusaslicer terminology for it. You can either turn it off (which will make your print a lot slower and might harm quality in some ways) or set "Max Comb Distance With No Retract" to something very small, like 1 mm. This will create a lot of additional retractions, and you need to make sure your retraction settings are right (in terms of distance and speed) not to make the problem worse - you can also ooze material while waiting around for a slow retraction to happen. Doing a retraction tuning tower can help you get them right if you don't have them right already. On an Ender 3 you should be able to set the retraction (and unretraction) speed to at least 100 mm/s, with distance somewhere around 4.0-6.5.
For readers using Cura, also be sure to set the "Minimum Extrusion Distance Window" option to 0. Otherwise Cura will start skipping retractions again once there are too many of them, which will bring the problem right back, possibly far worse since it might skip them even in the places they matter most. I don't think Prusaslicer has such a problem but I'm not sure.
What I have done:
All of those don't solve this issue. Then I realized that while my z motor rotates there were some occasions where the rod wasn't rotates. I changed the hex bolts and tighten them up properly to solve this issue.