Body weight support treadmill training (BWSTT) can improve motor function of lower limb in stroke patients, but it is not clear the underlying biomechanical contributors to these improvements. The purpose of this study was to evaluate changes of thigh muscle architecture parameters after stroke and compare the effect of BWSTT and traditional walking training at muscle fascicle level by using ultrasonography. This study showed that there are considerable changes in the thigh muscle architecture poststroke, which may contribute directly to muscle weakness and impaired motor functions in stroke survivors. BWSTT can improve the motor function of subacute stroke patients by change the muscle architecture and it is feasible and more effective than conventional gait training with regard to clinical scales. In addition, muscle ultrasound is an excellent tool for quantifying muscle changes in stroke patients.