Functional electrical stimulation (FES) is a neuroprosthetic technique to help restore motor function of spinal cord-injured (SCI) patients. Through delivery of electrical pulses to muscles of motor-impaired subjects, FES is able to artificially induce their muscle contractions. Evoked electromyography (eEMG) is used to record such FES-induced electrical muscle activity and presents a form of $M$-wave. In order to monitor electrical muscle activity under stimulation and ensure safe stimulation configurations, closed-loop FES control with eEMG feedback is needed to be developed for SCI patients who lose their voluntary muscle contraction ability. This work proposes a closed-loop FES system for real-time control of muscle activation on the triceps surae and tibialis muscle groups through online modulating pulse width (PW) of electrical stimulus. Subject-specific time-variant muscle responses under FES are explicitly reflected by muscle excitation model, which is described by Hammerstein system with its input and output being, respectively, PW and eEMG. Model predictive control is adopted to compute the PW based on muscle excitation model which can online update its parameters. Four muscle activation patterns are provided as desired control references to validate the proposed closed-loop FES control paradigm. Real-time experimental results on three able-bodied subjects and five SCI patients in clinical environment show promising performances of tracking the aforementioned reference muscle activation patterns based on the proposed closed-loop FES control scheme.