There is little known about kinetic changes in anterior cruciate ligament deficiency (ACLD) combined with meniscal tears during jogging. Therefore, 29 male patients with injured ACLs and 15 healthy male volunteers were recruited for this study to investigate kinetic abnormalities in male patients after ACL deficiency combined with a meniscal injury during jogging. Based on experimental data measured by an optical tracking system, a subject-specific musculoskeletal model was employed to estimate the tibiofemoral joint kinetics during jogging. Between-limb and interpatient differences were compared by the analysis of variance. The results showed that decreased knee joint forces and moments of both legs in ACLD patients were detected during the stance phase compared to the control group. Meanwhile, compared with ACLD knees, significantly fewer contact forces and flexion moments in ACLD combined with lateral and medial meniscal injury groups were found at the mid-stance, and ACLD with medial meniscal injury group showed a lower axial moment in the loading response (p < 0.05). In conclusion, ACLD knees exhibit reduced tibiofemoral joint forces and moments during jogging when compared with control knees. A combination of meniscus injuries in the ACLD-affected side exhibited abnormal kinetic alterations at the loading response and mid-stance phase.