We propose several simple numerical indices for representing structural difference between molecular graphs, which is based on vertex difference and edge difference. In this work, we simply employed molecular graphs which all of their simple graph representations are isomorphic. The vertex difference describes the difference in terms of atom type on the same simple graph molecular framework. The edge difference describes the difference in terms of bond type. Alternatively, chemical structure difference was also defined that describes the difference of both atom type and bond type. We employed these indices for similar structure searching. The results showed that the structure-difference based searching gives us similar structure searching that is considerably different from conventional methods.