Deep‐level defects in Li+‐implanted ZnSe epilayer grown by metalorganic vapor‐phase epitaxy (MOVPE) on a GaAs substrate have been characterized by using the deep‐level transient spectroscopy method under different post‐implantation annealing conditions. Four electron traps with energy levels ofEc−0.3, 0.33, 0.55, and 1.02 eV and one hole trap with an energy level ofEv+0.23 eV were detected. Possible physical origins and formation mechanisms for these defects were discussed using the defect model proposed by Myles and Sankey [Phys. Rev. B29, 6810 (1984)]. The results showed that interdiffusion between the ZnSe/GaAs heterointerface plays an important role on the formation of native defects in the MOVPE‐grown ZnSe epitaxial films on the GaAs substrate.