As mentioned in comments, one has to think not of sub-root systems, but rather of "quotients" of root systems here. As also mentioned in a comment, there is some activity on this topic under the name of "folding" in recent years, but I think it is not explored in the generality that it could be. Cf. https://math.stackexchange.com/a/3972084/96384, https://math.stackexchange.com/a/3300945/96384 and links from there.
In fact, as Callum suggests: Choose a set of simple roots $\gamma_1, \gamma_2, \gamma_3$ for $B_3$, where $\gamma_3$ is the short root. Now "mod out" the relation $\gamma_1=\gamma_3$, i.e. project the ambient, three-dimensional space down to the plane orthogonal to $\gamma_1-\gamma_3$.
If we call $\alpha$ the image of $\gamma_1$ (and $\gamma_3$) under this projection, and $\beta$ the image of $\gamma_2$, one easily checks that all positive roots of $B_3$ get projected to $\alpha$, $\beta$, $\alpha+\beta$, $2\alpha+\beta$, $3\alpha+\beta$, $3\alpha+2\beta$, i.e. the projection/quotient/folding is a root system of type $G_2$ with $\alpha$ (short) and $\beta$ (long) forming a set of simple roots. (If one chooses Cartesian coordinates for better visualization, say $\gamma_1 = (0,-1,1), \gamma_2= (-1,1,0), \gamma_3 = (1,0,0)$, then we project down to the plane $z=x+y$ (which already contains $\gamma_2$ but is perpendicular to $(1,1,-1) = \gamma_3-\gamma_1$.)
To bring things back up to the Lie algebra or group level, cf. the near-duplicate Understanding $G_2$ inside Spin(7)? (EDIT: problem solved).
What makes this specific "folding" a bit strange compared to the standard first examples is that it is not induced by any kind of automorphism of the roots; in fact, we identified the long root $\gamma_1$ with the short root $\gamma_3$! Maybe it becomes more plausible if one sees $B_3$ already as a folding of $D_4$ (as mentioned in Travis Willse's comment). This $D_4$, its Dynkin diagram being "three branches from a central node" seems to play the role of kind of a "simply laced covering" for both $B_3$ and $G_2$: For $D_4 \twoheadrightarrow B_3$, one identifies two of the outer nodes of $D_4$ (and similarly one always gets $D_{n+1} \twoheadrightarrow B_n$); whereas for $D_4 \twoheadrightarrow G_2$, one identifies all three of the outer nodes of $D_4$. What we are doing here is factoring the second folding through the first: which explains why we had to identify that remaining one-edged branch of the diagram with the two-edged one on the other side, the central node $\gamma_2$ has to stay long, whatever it takes.