Objective To observe the effects of 12-week pilates exercise and trunk strength training on the scores of visual analog scale (VAS) and Roland-Morris disability questionnaire (RMDQ), trunk extension/ ?exion strength and dynamic balance of female college students with chronic non-specific low back pain (CNSLBP), so as to offer a practical-based evidence for the rehabilitation treatment for female college students with CNSLBP. Methods A total of 45 female college students with CNSLBP were randomly divided into pilates (n = 22) and strength training groups (n = 23). Then, the scores of VAS and RMDQ, trunk extension/?exion strength and dynamic balance were measured before and after the exercise. Results After the 12-week exercise program, compared with the pre-exercise period, the VAS and RMDQ scores in the pilates and strength training groups were significantly decreased; the extensor peak torque (EPT) at 30°/s and 90°/s angular velocities in both groups and the flexor peak torque (FPT) at 90°/s angular velocities in the Pilates group were significantly increased, and the ratio of flexor/extensor (F/E) at 30°/s and 90°/s angular velocities in both groups were significantly decreased. In the eyes-open condition, only the anterior/posterior stability index (APSI) significantly decreased in the Pilates group. With eyes closed, the APSI, stability index (SI), and medial/lateral stability index (MLSI) significantly decreased in the pilates group, and only the APSI significantly decreased in the strength training group. After 12-week exercise, compared with strength training group, the VAS scores and F/E at 30°/s and 90°/s angular velocities decreased significantly in the pilates group, and EPT at 30°/s and 90°/s angular velocities increased significantly. In the eyes-closed condition, the SI, APSI, and MLSI in the pilates group were significantly lower than those in strength training group. Conclusions Compared with strength training, pilates exercise can significantly increase and balance the trunk flexion/extension muscle strength of female college students with NSLBP, enhance dynamic balance ability under eyes-closed conditions, and improve the low back pain of CNSLBP female college students with CNSLBP.