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Abstract Decoding movement intentions from motor unit (MU) activities to represent neural drive information plays a central role in establishing neural interfaces, but there remains a great challenge for obtaining precise MU activities during sustained muscle contractions. In this paper, we presented an online muscle force prediction method driven by individual MU activities that were decomposed from prolonged surface electromyogram (SEMG) signals in real time. In the training stage of the proposed method, a set of separation vectors was initialized for decomposing MU activities. After transferring each decomposed MU activity into a twitch force train according to its action potential waveform, a neural network was designed and trained for predicting muscle force. In the subsequent online stage, a practical double-thread-parallel algorithm was developed. One frontend thread predicted the muscle force in real time utilizing the trained network and the other backend thread simultaneously updated the separation vectors. To assess the performance of the proposed method, SEMG signals were recorded from the abductor pollicis brevis muscles of eight subjects and the contraction force was simultaneously collected. With the update procedure in the backend thread, the force prediction performance of the proposed method was significantly improved in terms of lower root mean square deviation (RMSD) of around 10% and higher fitness (R2) of around 0.90, outperforming two conventional methods. This study provides a promising technique for real-time myoelectric applications in movement control and health.