I know that for isomorphism between two groups we check one to one, onto mapping and homomorphism between them. I want to know how to find the number of isomorphic subgroup of two groups.
i assume that the question you are asking can be formalized in the following way: given two finite groups G and H, how many pairs (A, B) are there with A subgroup G and B subgroup H and A is isomorphic to B?
the first clear limitation is that the subgroup orders |A| = |B| must divide gcd(|G|, |H|), but that is a very weak condition (though it can be enough, e.g., when the gcd is 1)
a simpler first cut might be the case G = H, which is to find the number of isomorphic pairs of subgroups of a given finite group, but i don't think this is even known for all p-groups (groups G with |G| = power of a prime p)
another special case is for abelian (commutative) groups, for which the problem can be reduced to the various p-groups, and, i suspect, a complete answer can be written
I don't think that this is a typical question, one can refine the question considerably (for instance take G =H to be an arbitrary p-group, and try find the number of subgroups of order p( which are all isomorphic)), and one is still far from a satisfactory answer.