This study aimed to assess the efficacy of a 12-week Baduanjin qigong training program in preventing bone loss for middle-aged women. An experimental design was adopted, and subjects were assigned randomly into an experimental group (n = 44) and a control group (n = 43). The experimental group received a 12-week Baduanjin qigong training program, whereas the control group did not. Interleukin-6 (IL-6) and bone mineral density (BMD) were measured before and after the intervention. The results showed significant differences in IL-6 (t = -5.19, p < 0.000) and BMD (t = 1.99, p = 0.049) between the groups. Baduanjin reduced IL-6 and maintained BMD in the experimental group. In conclusion, this study demonstrates promising efficacy of Baduanjin in preventing bone loss commonly occurring in middle-aged women. Thus, Baduanjin is valuable for promoting and maintaining the health status of middle-aged women.