In this present study, we demonstrated that TgCDPK3 interacts with autophagy related proteins Atg3 and Atg5 to recruit immune-related proteins IRGs and GBPs on PV membrane during the infection with macrophage of the type II strain, which is beneficial to the less virulent strain of T. gondii long-term latency in host cells. This evidence concerns the gene ATG3 and infection.