Background Studies on professional identity and related factors among Chinese general practitioners (GPs) are unavailable. The objective of this study was to investigate the professional identity level of GPs in China and explore factors associated with GPs' perceptions of their professional identity. Methods A multistage stratified random sampling method was used to collect data with a structured self-administered questionnaire from 3236 GPs working in community health service institutions (CHIs) in China between October, 2017 and February, 2018. Professional identity was measured by the 13 items scale. Descriptive statistics were calculated and groups' differences were estimated using nonparametric tests. Multiple linear stepwise regression analysis was used to analyze factors associated with professional identity among GPs. Results Based on a total score of 65 on the professional identity scale, the average score for GPs' professional identity was 51.23 (SD = 6.56). Multiple linear stepwise regression analysis showed that GPs who practiced in Central China, with an administrative responsibility, at a moderate or higher income level, who frequently worked overtime, had more occupational development opportunities, with a higher level of job satisfaction and older GPs had higher levels of professional identity. Conclusions Professional identity level among GPs in China is high. Region, administrative responsibility, income level, working overtime, occupational development opportunities, age, and job satisfaction were significant predictors of professional identity.