With the molecular dynamics method, this paper investigates radiation-induced defects in the In0.16Ga0.84N/GaN superlattice structure (SLS) and the In0.04Ga0.96N/GaN SLS. In the temporal evolution of cascades, most of vacancies recombine with interstitials. The Monte Carlo simulations about the proportions of PKAs induced by 3 MeV protons were also considered in this work for calculating the weighted averages of surviving defects. For the In0.16Ga0.84N/GaN SLS irradiated by protons, around 82.6 percent of surviving vacancies are Ga vacancies while around 88.9 percent of surviving interstitials are Ga interstitials. For the In0.04Ga0.96N/GaN SLS irradiated by protons, around 87.3 percent of surviving vacancies are Ga vacancies while around 88.6 percent of surviving interstitials are Ga interstitials. N vacancies, N interstitials, and In vacancies also exist in irradiated InGaN/GaN SLS. Details about different types of defects are presented in this paper, which helps explain the microscopic mechanism of irradiated InGaN/GaN SLS. Since different types of defects have different influences on electronic and optical properties, simulations about the proportions of various defects in irradiated InGaN/GaN SLS help experimentalists find the effective factors of radiation-related changes in electronic and optical properties.