Muscle fatigue significantly impacts coordination, stability, and speed in daily activities. Accurate assessment of muscle fatigue is vital for effective exercise programs, injury prevention, and sports performance enhancement. Current methods mostly focus on individual muscles and strength evaluation, overlooking overall fatigue in multi-muscle movements. This study introduces a comprehensive muscle fatigue model using non-negative matrix factorization (NMF) weighting. NMF is employed to analyze the duration multi-muscle weight coefficient matrix (DMWCM) during synergistic movements, and four electromyographic (EMG) signal features in time, frequency, and complexity domains are selected. Particle Swarm Optimization (PSO) optimizes feature weights. The DMWCM and weighted features combine to calculate the Comprehensive Muscle Fatigue Index (CMFI) for multi-muscle synergistic movements. Experimental results show that CMFI correlates with perceived exertion (RPE) and Speed Dynamic Score (SDS), confirming its accuracy and real-time tracking in assessing multi-muscle synergistic movements. This model offers a more comprehensive approach to muscle fatigue assessment, with potential benefits for exercise training, injury prevention, and sports medicine.