Objective To explore the teaching effect of research ability training course on the improvement of research capacity of undergraduates majoring in basic medicine. Methods The questionnaire survey was used. From April 2017 to June 2019, 163 students of 8-year program enrolled from 2014 to 2016 in Peking University were selected as the research objects. The self-rating scale of research capacity was used to evaluate the students' capacity before and after the training course. A questionnaire survey was applied to evaluate the teaching effect of the course. Descriptive analysis, correlation analysis, Mann-Whitney test and paired sample Wilcoxon test were used to analyze the changes of students' scientific research capacity before and after the course and to identify the influencing factors. Results The self-evaluation of students' scientific research capacity [(107.9±11.3) vs. (102.0±12.5)] was significantly improved after the course. The self-evaluation scores of the students in the active group were significantly higher than those in the inactive group no matter before the course [(107.2±12.2) vs. (96.6±12.1)] or after the course [(111.6±11.1) vs. (104.2±12.2)]. Correlation analysis showed that students' experience in scientific research practice (ρ=0.243), students' attitude to the course (ρ=0.299) and teaching evaluation score (ρ=0.264) were significantly and positively correlated with the self-evaluation score of scientific research capacity after the course. The teacher guidance (weighted proportion 61.7%) was of great importance for promoting the improvement of students' scientific research capacity. Conclusions The research capacity training course based on research project design promotes the capacity building for research by undergraduates. Teacher guidance and students' active attitude of participation are quite important to guarantee the learning outcome of the course.