Muscle fatigue analysis has been an important topic in sport and rehabilitation medicine due to its role in muscle performance evaluation and pathology investigation. This paper proposes a surface electromyography (sEMG) based muscle fatigue analysis approach which was specifically designed for stroke rehabilitation applications. 14 stroke patients from 5 different Brunnstrom recovery stage groups were involved in the experiment and features including median frequency and mean power frequency were extracted from the collected sEMG samples for investigation. After signal decomposition, the decline of motor unit firing rate of patients from different groups had also been studied. Statistically significant presence of fatigue had been observed in deltoideus medius and extensor digitorum communis of patients at early recovery stages (P<;0.05) and no similar observation had been obtained for patients at later stages (P>0.01). It had also been discovered that the motor unit firing frequency declines with a range positively correlated to the recovery stage during repetitive movements. Based on the experiment result, it can be verified that as the recovery stage increases, the central nervous system's control ability strengthens and the patient motion becomes more stable and resistive to fatigue.