Background Psychological and physical problems regarding the quality of life (QOL) of doctors have attracted increasing attention in recent years, especially in China. The objective of this study was to measure the mental health and physical fitness of young clinical doctors with the SF-36 and to evaluate related psychometric properties and factors.Subjects and methods Young doctors from Guizhou Provincial People’s Hospital completed the SF-36 between November 1, 2017, and February 28, 2018. The Physical Component Summary (PCS) and Mental Component Summary (MCS) were measured to represent physical and mental health conditions.Results A total of 444 doctors aged 20–40 years, with 138 (31.08%) surgeons, 110 (24.77%) physicians, 26 (5.86%) pediatricians, 28 (6.31%) obstetricians/gynecologists and 142 (31.98%) doctors from other departments were enrolled in this study, and their data were analyzed. The mean PCS scores (71.30 ± 16.54 vs. 77.54 ± 15.96, p < 0.0001) and MCS scores (63.72 ± 18.91 vs. 71.29 ± 17.86, p < 0.0001) were significantly lower than the normative values of Chinese respondents. Pediatricians and obstetricians/gynecologists reported the lowest PCS and MCS scores. Young doctors with master’s degrees and above (OR = 1.68, 95%CI: 1.03–2.75, p < 0.05), those who were unmarried (OR = 2.40, 95%CI: 1.40–4.08, p < 0.01), and those who had low family incomes (OR = 2.45, 95%CI: 1.00-6.01, p < 0.05) had increased odds of poor MCS scores.Conclusions Poor mental and physical health were common in young doctors in China. Pediatricians and obstetricians/gynecologists had the poorest physical and mental health status. Having a high education level, being unmarried and having a low family income were negatively associated with mental health.