Functional electrical stimulation (FES) is effective to restore movement in spinal cord injured (SCI) subjects. Unfortunately, muscle fatigue constrains the application of FES so that output torque feedback is interesting for fatigue compensation. Whereas, inadequacy of torque sensors is another challenge for FES control. Torque estimation is thereby essential in fatigue tracking task for practical FES employment. In this work, the Hammstein cascade with electromyography (EMG) as input is applied to model the myoelectrical mechanical behavior of the stimulated muscle. Kalman filter with forgetting factor is presented to estimate the muscle model and track fatigue. Fatigue inducing protocol was conducted on three SCI subjects through surface electrical stimulation. Assessment in simulation and with experimental data reveals that the muscle model properly fits the muscle behavior well. Moreover, the time-varying parameters tracking performance in simulation is efficient such that real time tracking is feasible with Kalman filter. The fatigue tracking with experimental data further demonstrates that the proposed method is suitable for fatigue tracking as well as adaptive torque prediction at different prediction horizons.