Abstract Background Men who have sex with men (MSM) are at high risk of human immunodeficiency virus (HIV) infection and sexually transmitted infection (STI) in China. Inadequate clinical services and poor clinical competency among physicians are major barriers to improving the sexual health of MSM. This study aims to understand physician clinical competency in providing MSM health services in China. Methods We conducted an online cross-sectional survey among Chinese physicians who have seen male patients for STI complaints in the past year. We obtained information on individual demographics, clinical practice, attitudes toward MSM, and interest in contributing to MSM clinical services. We defined an MSM-competent physician as one who asked male patients about sexual orientation, sexual practices, and recommended HIV/ STI testing during a clinic visit. We conducted multivariable logistic regression to identify factors associated with MSM competency. Results In total, 501 physicians completed the survey. The most common subspecialties were dermatovenereology (33.1%), urology (30.1%), and general medicine (14.4%). Roughly half (n = 267, 53.3%) reported seeing MSM in the past 12 months. Among physicians who saw MSM in the past 12 months, 60.3% (n = 161) met criteria as MSM-competent physicians, and most (n = 234, 87.6%) MSM-competent physicians reported positive or neutral attitudes towards MSM. Over 60% of all physicians were willing to participate in activities for improving MSM services, such as training and being on a list of physicians willing to serve MSM. MSM-competent physicians showed no sociodemographic differences compared with non MSM-competent physicians. MSM-competent physicians were more willing to have their medical institution named on a public clinic list capable of serving MSM (aOR: 1.70, 95%CI: 1.01–2.86) and being on a public physician list capable of serving MSM (aOR: 1.77, 95%CI: 1.03–3.03). Conclusions MSM-competent physicians included a broad range of individuals that practiced in diverse clinical settings. Most physicians were interested in improving and expanding MSM clinical services, despite having neutral attitudes toward same-sex behavior. Future interventions should focus on developing MSM clinical competency and expanding services that meet the needs of MSM.