To explore the changes in the mental health levels of Chinese physical education college students, the present study conducted a cross-temporal meta-analysis of 43 papers that adopted the Symptom Checklist 90 (SCL-90) from 1995 to 2019. The results showed that the average scores of the seven SCL-90 factors were negatively correlated with the year of data collection. The socioeconomic indicators (GDP, per capita GDP and household consumption level) were significantly negatively correlated with the eight dimension scores of the SCL-90 (except for phobic anxiety). The mean effect sizes of the sex differences in the seven dimension scores (except depression and phobic anxiety) were lower than the small effect size. In conclusion, Chinese physical education college students’ mental health levels have increased in the past 25 years. This phenomenon may be related to Chinese socioeconomic growth, the implementation of national sports policies, and the provision of mental health education for college students. In addition, although the increasing trend in the mental health level of female students was more obvious, there were no significant sex differences.