Identification of human immunodeficiency virus (HIV) transmission networks is a critical step in the public health response; however, it is challenging to achieve this through traditional epidemiological surveys alone. The molecular network approach can provide more accurate information for understanding HIV outbreaks and bring targeted interventions into reality. Based on the current global development of the concept of the molecular network, Chinese scientists have in recent years explored the applications of molecular networks for understanding the HIV-1 transmission trends, for identifying the population acquiring priority interventions, and for evaluating the targeted intervention effectiveness. In this review, we focus on research progress by Chinese scientists in the field of molecular networks and put forward some suggestions for future research of molecular networks.