By making use of the U(1) gauge potential decomposition theory and the phi-mapping topological current theory, we investigate the Schrodinger-Chern-Simons model in the thin-film superconductor system and obtain all exact Bogomolny self-dual equation with a topological term. It is revealed that there exist self-dual vortices in the system. We study the inner topological structure of the self-dual vortices and show that their topological charges are topologically quantized and labeled by Hopf indices and Brouwer degrees. Furthermore, the vortices are found generating or annihilating at the limit points and encountering, splitting or merging at the bifurcation points of the vector field phi.