Due to the significant non-stationarity and feature distribution discrepancies in surface electromyography (sEMG) signals during muscle fatigue monitoring, traditional fixed-parameter Transformer models often struggle to accurately capture the complex evolution of time-frequency characteristics across different fatigue stages. To address this limitation, this paper proposes a K-means clustering-guided neural architecture search method (CG-NAS) to achieve adaptive optimization of Transformer architectures based on data distribution characteristics. The method first classified input EMG features using the K-means clustering algorithm and constructed Gaussian distributions characterized by mean and variance to quantify the complexity of each cluster. These distribution priors then guided the neural architecture search process, enabling dynamic alignment between the architecture search space and data characteristics: for low-complexity data clusters with small mean and variance, lightweight Transformer architectures were selected, whereas for high-complexity clusters, architectures with greater width and depth were allocated. Experimental results demonstrated the superior performance of CG-NAS in muscle fatigue index prediction tasks, achieving a mean absolute error of 0.098 2 and a coefficient of determination of 0.957 3, significantly outperforming multiple benchmark models. The study shows that CG-NAS effectively aligns with the nonlinear evolution of time-frequency features during the fatigue process and provides an efficient and robust solution for fatigue monitoring.