This might be a very trivial question, and I have explained what I think about it below. Let's say I have an automorphism $f : H \to H$. Now, let's say I take two subgroups $G_1$ and $G_2$ of $H$. Is it necessary that $f: G_1 \to G_2$ is also an isomorphism?
I think yes, cause all the elements of $G_1$ and $G_2$ are still the elements of H, and if $f$ is an automorphism, $f: G_1 \to G_2$ should necessarily be an isomorphism too.
Edit: Originally, I forgot to say that the two subgroups $G_1$ and $G_2$ have same cardinality.
If you're assuming that $\text{Im}(f|_{G_1}) \subseteq G_2$ (otherwise the question doesn't really make any sense), then the answer is yes if $G_1$ is finite and not necessarily otherwise.
If $G_1$ is finite, then since $f$ is monomorphism, $f : G_1 \to G_2$ is also a monomorphism and a monomorphism between two finite groups of the same cardinality is an isomorphism.
If $G_1$ can be infinite, we can take $H = \bigoplus_{n \in \mathbb{N}} \mathbb{Z}, \ G_1 = \{0\} \ \oplus \ \bigoplus_{n \geq 1}\mathbb{Z}, \ G_2=H$ and $f = 1_H$. Then $f : G_1 \to G_2$ is not surjective but $G_1$ and $G_2$ have the same cardinality.