Abstract Background Percutaneous endoscopic lumbar discectomy (PELD) is a promising minimally invasive treatment for lumbar disc herniation (LDH). Postoperative rehabilitation can improve patient outcomes. Not only rehabilitation for surgical trauma but also rehabilitation for lumbar spine and lower kinetic chain dysfunction should be performed. The aims of this study were to investigate the efficacy of a lumbar kinetic chain training for staged rehabilitation after PELD for LDH. Methods Fifty one LDH patients treated with PELD were studied. After surgery, patients underwent lumbar kinetic chain training for staged rehabilitation( staged group) or regular low back rehabilitation (regular group). The staged rehabilitation programme included three phases from 2 to 6, 7–12, and 13–24 weeks postoperatively, and different physical therapies were performed during these phases. The low back pain visual analogue scale (VAS), JOA score, ODI, SF-36, and cross-sectional area of the lumbar multifidus on MRI were assessed, and gait analysis was performed. Results Twenty five patients in staged group and twenty six patients in regular group were included. There were no significant differences in age or sex between the two groups at baseline ( p  > 0.05). The VAS score decreased and the JOA and SF-36 scores increased in both groups from baseline to 6 weeks ( P  < 0.05). In the staged group, compared with the regular group, the VAS and ODI scores were lower and the JOA and SF-36 scores were higher at 6 weeks ( P  < 0.05); the VAS and ODI scores were lower and the SF-36 score was higher at 12 weeks ( P  < 0.05); the SF-36 score was higher at 24 weeks ( P  < 0.05); the cross-sectional area of the lumbar multifidus showed no differences at 12 weeks ( P  > 0.05); and the left-right support ratio of gait was higher at 24 weeks ( P  < 0.05). Conclusions The staged rehabilitation programme for LDH after PELD promoted postoperative recovery, and the efficacy of lumbar kinetic chain training was higher than that of regular low back muscle exercise.