To investigate the prevalence and the associated risk factors of human immunodeficiency virus (HIV), hepatitis B virus (HBV) and sexually transmitted infections (STIs) among men who have sex with men (MSM) in Kunming, 300 MSM were recruited through community-based organizations between September 2014 and January 2015. The prevalence of HIV, HBsAg, syphilis, Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) were 17.0%, 7.7%, 11.3%, 18.2% and 13.2%, respectively. In the three different anatomic sites (urethra, rectum and pharynx), the prevalence of rectal CT was the highest (15.5%), whereas NG was most commonly found in the pharynx (8.1%). Low education level, homosexuality, inconsistent condom use and drug use in the previous six months were significantly associated with HIV infection, whereas the former three factors were also associated with HBV infection.Older people (aged ≥ 40 years) and those who lacked knowledge of STIs, and younger people (aged <30 years) as well as inconsistent condom users were more at risk of syphilis and CT infections, respectively. NG infection was only associated with reported dating venues. Our study revealed a heavy disease burden and multiple risk factors of HIV/STIs among MSM in Kunming. It is necessary to promote regular screening and proactive treatment of HIV/STIs among MSM.