This review aimed to evaluate the effectiveness and safety of Baduanjin qigong on perimenopausal and postmenopausal symptoms based on clinical trials. A literature search was conducted in 7 databases up to June 30, 2023. The information of study design and observed indicator based on perimenopausal and postmenopausal stage was extracted. We mainly analyzed the effectiveness, safety and the methodology quality. Thirty-five trials were selected, and 17 original studies were considered good methodological quality. During perimenopause, Baduanjin was mainly to treat mood disorders (63.64%, 14/22), among which 6 (42.86%, 6/14) were depression, 2 (14.29%, 2/14) were depression and anxiety, and 1 (7.14%, 1/14) was anxiety, as well as 5 (35.71%, 5/14) sleep disorders. And the exercise program had a duration of 45 to 50 minutes (57.14%, 8/14), 7 times (71.43%, 10/14) a week. The programs lasting 3 months (42.86%, 6/14), accounted for the highest proportion of the exercise program. In the postmenopausal stage, Baduanjin was used to treat osteoporosis (84.62%, 11/13). From the data available, the program with 2 to 3 times a day (81.82%, 9/11) reported the highest number of significant effects, with a maximum duration of 12 months (55.56%, 5/9), followed by 6 months (33.33%, 3/9). A total of 8 trials mentioned the adverse reactions, but none was related to Baduanjin, and the dropout of participants (1.96%, 57/2912) was also not associated with Baduanjin. There is evidence for positive effects of Baduanjin in addressing perimenopausal mental disorders and postmenopausal osteoporosis, but more research is necessary to clarify best practices and quantify results.