A model-based FES would be very helpful for the adaptive movement synthesis of spinal-cord-injured patients. For the fulfillment, we need a precise skeletal muscle model to predict the force of each muscle. Thus, we have to estimate many unknown parameters in the nonlinear muscle system. The identification process is essential for the realistic force prediction. We previously proposed a mathematical muscle model of skeletal muscle which describes the complex physiological system of skeletal muscle based on the macroscopic Hill-Maxwell and microscopic Huxley concepts. It has an original skeletal muscle model to enable consideration for the muscular masses and the viscous frictions caused by the muscle-tendon complex. In this paper, we present an experimental identification method of biomechanical parameters using Sigma-Point Kalman Filter applied to the nonlinear skeletal muscle model. Result of the identification shows its effective performance. The evaluation is provided by comparing the estimated isometric force with experimental data with the stimulation of the rabbit medial gastrocnemius muscle. This approach has the advantage of fast and robust computation, that can be implemented for online application of FES control.