Abstract Background Physiological and metabolic processes are influenced by biological rhythms. However, whether exercising in the morning or evening is more beneficial, given that these periods are two key time windows to incorporate exercise, has remained unclear. This study aimed to investigate the effects of morning versus evening exercise on weight loss, morphometric indicators, and physical fitness among Chinese college students with overweight and obesity. Methods A total of 31 students with overweight and obesity (18–22 years old) were randomly assigned to exercise in the morning (7 am to 10 am, n = 16) or evening (6 pm to 9 pm, n = 15). The morning exercise group had an average age of 19.69 ± 1.01 years and a body mass index (BMI) of 27.13 ± 2.66 kg/m². The evening group had an average age of 19.47 ± 0.99 years and a BMI of 27.91 ± 3.40 kg/m². In the morning group, 87.5% of participants were male, while 73.3% were male in the evening group. The intervention was aerobic running exercise for 60 min, five times a week for 10 weeks. Measurements were taken before and after the 10-week intervention. Results The BMI values of male and female college students were significantly and positively associated with vital capacity (p