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To understand the epidemiology, evolutionary and transmission characteristics of HIV‐1 CRF07_BC in Nanjing, China. One hundred and fifty‐nine patients with HIV‐1 CRF07_BC were recruited. DNA sequencing, phylogenetic analysis, and molecular transmission cluster analysis were conducted to determine the molecular epidemiology and evolutionary characteristics. Of these HIV‐1‐infected patients, 95.6% were male, and men who sex with men (76.7%) were the main transmission route. Only 34.0% of these cases were born in Nanjing, and most of them (64.8%) reported having multiple sex partners in the last 6 months. The maximum likelihood phylogenetic analyses of HIV‐1 CRF07_BC revealed two lineages. Overall, 67.3% of Nanjing sequences were connected to at least one other individual distributed in 11 clusters, and the average degree was 21.2 with range (1‐178). The clustered patients were more likely to be male. The time to a most recent common ancestor for the early HIV‐1 CRF07_BC circulating in Nanjing was estimated to be 1998.71[1997.36‐2001.07]. The mean estimated evolutionary rate for the epidemic cluster was slightly lower at 2.38[2.12‐2.65] × 10−3 per site per year with the relaxed exponential clock model. HIV‐1 CRF07_BC was transmitted into Nanjing more than 20 years ago from Yunnan and has become one of the most predominant subtypes with a higher evolutionary rate than before. Highlights: We performed a comprehensive phylodynamic analysis of HIV‐1 CRF07_BC sequences from Nanjing.HIV‐1 CRF07_BC was transmitted into Nanjing more than 20 years from Yunnan.There were two waves of HIV‐1 CRF07_BC infection transmitted to Nanjing.MSM may have significantly contributed to the complicated transmission pattern of HIV‐1 CRF07_BC. [ABSTRACT FROM AUTHOR]