Gait asymmetries after anterior cruciate ligament reconstruction (ACLR) may lead to radiographic knee osteoarthritis (OA) and secondary injury. This study aimed to investigate three-dimensional (3D) lower limb joint kinetics using a multi-body dynamic analysis method based on a subject-specific musculoskeletal model during level walking 2 years after ACLR. A total of 23 patients (2 females and 21 males) 2 years after ACLR were selected and underwent gait testing. 3D motion joint reaction forces and the internal moments of the hip, knee, and ankle joints for the stance phase of each gait cycle were calculated by a musculoskeletal multibody dynamics model. In the hip and ankle joints, the peak of the first anteroposterior forces on the affected side were significantly smaller compared to the non-affected side (both p ​= ​0.04). The abduction (peak2: p ​= ​0.01) and the internal rotation moment (peak1: p ​= ​0.02; peak2: p ​= ​0.01) of the affected knee were significantly smaller than the non-affected side, but both of them did not reach the Minimal clinically important difference. The external rotation moment of the affected ankle moments was greater than the affected side (p ​< ​0.01). Two years after ACLR, there was no clinically significant kinetic abnormality in the affected knee joint, the kinetics of the hip and ankle joint were still abnormal, which may lead to the development of OA and secondary injury. Gait retraining should be used to improve the kinetics of the hip, knee, and ankle after ACLR.