Dearth of information regarding the trend and correlates of HIV, syphilis and Hepatitis C (HCV) in a country-wide sample of understudied though high-risk Chinese men who have sex with men (MSM) called for a comprehensive serial cross-sectional study. Using a multistage mixed-method strategy, 171,311 MSM from 107 selected cities/counties in 30 provinces of mainland China, were interviewed and tested. Descriptive, bivariate, multivariate and Cochran-Armitage trend analyses were conducted using SAS 9.2. During 2009-13, recent (71.5% to 78.6%, p < 0.001) and consistent (40.4% to 48.8%, p < 0.001) condom use as well as condom use during commercial anal sex (46.5% to 55.0%, p < 0.001) were increasing. In contrast, commercial anal sex with male (11.9% to 7.1%, p < 0.001) and drug use (1.9% to 0.8%, p < 0.001) were decreasing over time. HIV prevalence increased gradually (5.5% to 7.3%, p < 0.001), while syphilis (9.0% to 6.3%, p < 0.001) and HCV prevalence (1.5% to 0.7%, p < 0.001) decreased over time. A positive correlation was observed between HIV and syphilis prevalence (r = 0.38). HIV infection was associated with HIV-related knowledge, services and injecting drug use. An increasing trend of HIV prevalence was observed during 2009-13 among MSM in China. While gradual reduction of risk behaviors along with syphilis and HCV prevalence supported expansion of testing and prevention services, increasing HIV burden called for deeper thematic investigations.