A study was conducted to investigate the effects of different levels of physical activity and circadian rhythm differences on the nine factors of obsessive-compulsive disorder, interpersonal sensitivity, depression, anxiety, hostility, phobia, paranoia, and psychoticism on the SCL-90 scale. A questionnaire and mathematical and statistical methods were used to conduct the study. Data were collected through a web-based cross-sectional survey of college students from three universities in Anhui. A statistical analysis of the collected data was conducted using mathematical and statistical methods. A total of 1248 students were included in the statistics of this study. Binary logistic regression analysis revealed that low physical activity levels were associated with somatization (OR = 1.36, 95% CI = 0.95-1.94), obsessive-compulsive disorder (OR = 1.85, 95% CI = 1.25-2.75), interpersonal sensitivity (OR = 1.94, 95% CI = 1.30-2.88), depression (OR = 2.03, 95% CI = 1.31-3.16), anxiety (OR = 1.67, 95% CI = 1.03-2.69), hostility (OR = 1.80, 95% CI = 1.12-2.89), phobia (OR = 1.88, 95% CI = 1.20-2.94), and paranoia (OR = 2.23, 95% CI = 1.43-3.46). Circadian rhythm differences were associated with somatization (OR = 0.91, 95% CI = 0.87-0.96), obsessive-compulsive disorder (OR = 0.93, p < 0.01, 95% CI = 0.89-0.98), interpersonal sensitivity (OR = 0.90, 95% CI = 0.85-0.94), depression (OR = 0.92, 95% CI = 0.87-0.97), anxiety (OR = 0.89, 95% CI = 0.83-0.95), hostility (OR = 0.91, 95% CI = 0.86-0.97), phobia (OR = 0.87, 95% CI = 0.82-0.93), and paranoia (OR = 0.90, 95% CI = 0.85-0.95) were all negatively associated. In addition, gender was associated with somatization and obsessive-compulsive disorder (OR = 0.75, 95% CI = 0.57-0.98), depression (OR = 0.92, 95% CI = 0.87-0.97), and paranoia (OR = 0.55, 95% CI = 0.40-0.76). Low-intensity physical activity was more likely to be associated with somatization, obsessive-compulsive disorder, relationship sensitivity, depression, anxiety, hostility, terror, and paranoia than high-intensity and moderate-intensity physical activity, and circadian rhythm differences showed that people who slept later (known as nocturnal) were more likely to have these problems.