A cross sectional survey was performed to investigate the epidemic of human immunodeficiency virus (HIV), hepatitis C virus (HCV), syphilis, and HIV-1 subtype infections among men who have sex with men (MSM) and to evaluate factors that were correlated with sexually transmitted infections (STIs) among 657 MSM in Zhenjiang, Jiangsu, during 2012-2013. Data on socio-demographic parameters and risky behaviors were collected, and blood samples were obtained. In this survey, the prevalence of STIs due to HIV (5.3%), HCV (0.6%), and syphilis (19.2%) were measured. Of 35 HIV-infected MSM, 1 (0.2%) and 17 (2.6%) were co-infected with HCV and syphilis. Among 33 samples with available HIV-1 genomic fragment sequences, 6.1% B, 72.7% CRF01_AE, and 21.2% CRF07_BC were identified. Multivariate logistic regression analysis showed that age > 30 years (odds ratio [OR] 2.002; 95% confidence interval [CI], 1.144-3.502) and having had STI symptoms in the past year (OR, 11.673; 95% CI, 3.092-44.078) were positively correlated with having an STI, while consistent use of a condom when having sex with male partners (OR, 0.621; 95% CI, 0.408-0.945) was significantly associated with a low STI rate. The worsening epidemic of HIV, HCV, and syphilis infections, and the prevalence of complex subtypes of HIV-1 and other risk factors suggest that effective intervention strategies should be strengthened for MSM in Zhenjiang, Jiangsu.