The cardinality is $\aleph_1$.
As noted by Andrés Caicedo, the nonscattered countable linear orders form a single $\sim$-class, so it suffices to explain why there are only $\aleph_1$-many $\sim$-classes of scattered types.
Rich Laver proved that the embeddability quasiorder of (countable) nonscattered types is a well-quasiorder. Call this quasiorder $W$. Let $P=W/\sim$ be the quotient poset. The poset $P$ has no infinite antichains or infinite properly descending chains. The task is to determine the size of $P$.
Recursively partition $P$ into levels: $L_0$ is the antichain of minimal elements of $P$, and for each $\alpha>0$, define $L_{\alpha}$ to be the antichain of minimal elements of $P-\bigcup_{\beta<\alpha} L_{\beta}$. Let $\gamma$ be the least ordinal that does not index any level. Then $|P| = |\bigcup_{\alpha<\gamma} L_{\alpha}| = |\gamma|$, since $\gamma$ is infinite and the levels are finite and partition $P$.
The question asks for the number of $\sim$-classes, which is the cardinality of $P$. We have just shown that this is $|\gamma|$. By Eric Wofsey's comment, $|\gamma|\geq \aleph_1$.
To obtain a contradiction, assume that $|\gamma|>\aleph_1$. Choose an ordinal $\delta$ so that $\aleph_1<\delta<\gamma$. Level $L_{\delta}$ is not empty, since $\delta<\gamma$, so pick a countable linear order $\Lambda_{\delta}$ so that $(\Lambda_{\delta}/\sim)\in L_{\delta}$. Every level $L_{\varepsilon}$, for $\varepsilon <\delta$, contains some $\Lambda_{\varepsilon}/\sim$, where $\Lambda_{\varepsilon}$ is a countable linear order embeddable in $\Lambda_{\delta}$. (If there exists some $\varepsilon < \delta$ whose level $L_{\varepsilon}$ does not contain the $\sim$-class of any poset embeddable in $\Lambda_{\delta}$, then the least-indexed level with this property would have to contain $\Lambda_{\delta}/\sim$, contradicting either $\varepsilon <\delta$ or the disjointness of the levels.)
But now we have a countable linear order $\Lambda_{\delta}$ which has $|\delta|$-many order types of pairwise $\sim$-inequivalent, countable linear orders that are embeddable into it, namely the $\Lambda_{\varepsilon}$'s. And remember that $\delta$ is uncountable. We have now obtained a contradiction to
Fraisse's Second Conjecture (also proved by Laver), which states that a countable scattered linear order has only countably many $\sim$-types of suborders. \\\\\
You will find the statements of all four of Fraisse's Conjectures on page 178 of Rosenstein's book Linear Orderings, Academic Press, 1982. The proof (due to Laver) of Fraisse's Second Conjecture is Theorem 10.52 of this book.