Unilateral transfemoral amputees rely heavily on non-amputated limb muscles to regulate the prosthetic gait. In this study, we compared the non-amputated limb muscle coordination of eight unilateral transfemoral amputees to eight able-bodied controls. Inverse dynamics approach was conducted via a musculoskeletal model to obtain lower limb joint moments and muscle forces. In addition to the muscle forces at the instants of peak joint moments and the maximum muscle forces, the peak joint moments of the lower limbs were also investigated. The results showed that there were significant differences of muscle forces between the non-amputated limbs and the controls at the instant of peak hip extension moment, although the peak hip extension moments themselves were not significantly different between the two groups. The non-amputated limbs had significantly smaller peak hip flexion moment and peak knee extension moment, with significant differences between the muscle forces of non-amputated limbs and controls at the two instants. There was no significant difference between the muscle forces of the non-amputated limbs and controls at the peak knee flexion moment instant, despite the fact that the non-amputated limbs had significantly higher peak knee flexion moments. In addition, the non-amputated limbs had significantly smaller maximum muscle forces than the controls. These results demonstrate that amputees modify their muscle coordination to adapt to the specific joint requirements of the prosthetic gait. Our findings suggest the possibility of non-amputated limb muscle atrophy due to the decrease in the peak muscle forces during walking.