Pathogen infection does not directly cause host death. Secondary infection is the main factor that leads to severe damage. Nuclear respiratory factor 1 (NRF1) is a nuclear transcription factor that regulate mitochondrial biogenesis. However, the function of NRF1 in antiviral immunity, especially its role in the process of co-infection is largely unknown. NRF1 inhibited virus infection by mediating apoptosis in arthropod, Procambarus clarkii. Notably, NRF1 expression was significantly induced in the early stage of white spot syndrome virus (WSSV) infection and reduced during the later stage of infection. NRF1 mediated apoptosis, phagocytosis, and reactive oxygen species (ROS) production 24 h after WSSV infection. The number of culturable bacteria was significantly increased and induced hypoxia in vivo 72 h after WSSV infection. Hypoxia exposure resulted in a decrease in NRF1 expression led to a decrease in body immunity and a vicious cycle until the crayfish died. This study demonstrated that secondary infections may be a major cause of biological mortality in crustaceans.