The reliable classification of motor unit action potentials (MUAPs) provides the possibility of tracking motor unit (MU) activities. However, the variation of MUAP profiles caused by multiple factors in realistic conditions challenges the accurate classification of MUAPs. The goal of this study was to propose an effective method based on the convolutional neural network (CNN) to classify MUAPs with high levels of variation for MU tracking. MUAP variation was added artificially in the synthetic electromyogram (EMG) signals and was induced by changing the forearm postures in the experimental study. The proposed overlapped-segment-wise EMG decomposition method and the spike-triggered averaging method were combined to obtain the MUAP waveform samples of individual MUs in the experimental study, and the MUAP profile classification performance was tested. Since the ground-truth of MU discharge activities was known for the synthetic EMG, the MU tracking performance was further verified by mimicking the tracking procedure of MU discharge activities and the spike consistency with the true spike trains was tested in the simulation study. The conventional MUAP similarity index (SI)-based method was also performed as comparison. For both the experimental and the synthetic EMG signals, the CNN-based method significantly improved the MUAP tracking performance compared with the conventional SI-based method manifested as a higher classification accuracy (93.3%±5.4% vs 56.2%±13.9%) in the experimental study or higher spike consistency (71.1%±10.2% vs 29.2%±11.0%) in the simulation study with a smaller variation. These results demonstrated the efficiency and robustness of the proposed method to distinguish MUAPs with large variations accurately. Further development of the proposed method can promote the study on the physiological and pathological changes of the neuromuscular system where tracking MU activities is needed.