Closed-loop management of athletes at the training base is a compromise approach that balanced epidemic prevention and sports training during the COVID-19 pandemic. This study investigated the impact of prolonged closed-loop management on athletes’ sleep and mood during the 2022 Shanghai Omicron wave. The Pittsburgh Sleep Quality Index and the Profile of Mood States were used to assess the sleep and mood states of 110 professional athletes in "closed-loop management" at the training base after 1 and 2 months of closed-loop management, respectively, to characterize changes in sleep and mood with prolonged closed-loop management. After two months of control, the sleep and mood of 69 athletes and students of the same age were measured using the Pittsburgh Sleep Quality Index and Perceptual Stress Scale, as well as the Warwick-Edinburgh Mental Well-being Scale, to compare the differences in sleep and mood between athletes undergoing closed-loop management and the general population who were managed in the community. Paired sample t-tests and independent sample t-tests were used for comparisons across different time intervals and different management approaches. Results showed that with the time of closed-loop management increased, athletes woke up earlier (p = 0.002), slept less (p = 0.024), and became angrier (p = 0.014); athletes had poorer overall sleep quality (p < 0.001) but lower stress level (p = 0.004) than those who were outside the base. In closed-loop management, the athletes were able to maintain a stable sleep and mood state. Sports team administrators must be aware of the need to improve athletes’ sleep quality and help athletes to agree with this approach of management.