Objective To evaluate clinical competency of trainees who attend standardized residency training (SRT) in municipal hospitals, and to provide data support for the work of SRT base. Methods From November to December 2019, a questionnaire survey was conducted among 380 physicians who attend SRT from at two prefecture-level hospitals in Hubei Province. Multiple linear regression was used to analyze the factors affecting the results on clinical competency. Results The score of clinical competencies in all participating physicians was (3.82±0.55), and the score in general practitioners (GPs) (3.59±0.56) was the lowest. The items with two lowest scores were research (3.28±0.83) and information management (3.41±0.59). Multiple linear regression analyses showed that, for trainees in the first year (b=-0.30) and the second year (b=-0.23)], their post competency scores were lower than those of trainees who had completed the training (all P<0.05). The competency score of GPs (b=-0.36) is lower than that of others (P<0.01). Conclusions Although this survey confirmed the effectiveness of SRT, weaknesses of clinical competency (e.g. academic research) were found in the trainees at municipal hospitals, particular for GPs. It is necessary to strengthen training specifically to fill the gap.