Objective To understand the current mental health status of pediatric resident trainees receiving standardized resident training and to explore the influencing factors. Methods The survey used a cross-section questionnaire based on Symptom Checklist 90 (SCL-90). In November 2021, the questionnaires were distributed to 326 pediatric resident trainees who received standardized resident training in Shenzhen Children's Hospital from 2018 to 2021. The survey data were analyzed by t-test, Kruskal-Wallis H test and logistic regression analysis. Results The total score of SCL-90 from the trainees was (127.6±34.4). The percentage of resident trainees with total score was more than 160 was 1.6% (5/311) and the percentage of trainees with positive items more than 43 was 2.6% (8/311). Among the factors, the positive rate of obsessive symptoms was the highest [46.9% (146/311)], followed by depression [28.0% (87/311)] and interpersonal sensitivity [24.1% (75/311)]. The score of obsessive symptom in socially recruited pediatric resident trainees (1.6±0.5) was significantly higher than that of postgraduates (1.5±0.6), P=0.044. The score of interpersonal sensitivity in trainees with community experience (1.3±0.4) was significantly lower than that of those without community experience (1.4±0.5), P=0.038. All scores from Grade 2020 trainees were significantly lower than those from trainees of Grade 2018 and 2019: the total score (116.2±21.9), (134.1±40.3) and (132.0±34.8); the score of obsessive symptoms (1.4±0.4), (1.7±0.7) and (1.6±0.3); depression (1.2±0.4), (1.5±0.4) and (1.5±0.5); interpersonal sensitivity (1.2±0.3), (1.4±0.3) and (1.4±0.3); anxiety (1.2±0.1), (1.4±0.4) and (1.4±0.5), all P<0.05. Multivariate analysis suggested that the grade (OR=1.813, 95%CI: 1.805-1.862) was a risk factor in mental health of pediatric resident trainees. Conclusions The mental health status of pediatric resident trainees is generally poor and the grade is the main influencing factor of their mental health. More attention should be paid to the mental health of trainees in the standardized resident training program.