Previous studies have shown that muscle repetitive stress injuries (RSIs) are often related to sport trainings among young participants. As such, understanding the mechanism of RSIs is essential for injury prevention. One potential means would be to identify muscles in risk by applying biomechanical modeling. By capturing 3D movements of four typical youth sports and building the biomechanical models, the current study has identified several risk factors related to the development of RSIs. The causal factors for RSIs are the muscle over-lengthening, the impact-like (speedy increase) eccentric tension in muscles, imbalance between agonists and antagonists, muscle loading frequency and muscle strength. In general, a large range of motion of joints would lead to over-lengthening of certain small muscles; Limb's acceleration during power generation could cause imbalance between agonists and antagonists; a quick deceleration of limbs during follow-throughs would induce an impact-like eccentric tension to muscles; and even at low speed, frequent muscle over-lengthening would cause a micro-trauma accumulation which could result in RSIs in long term. Based on the results, the following measures can be applied to reduce the risk of RSIs during learning/training in youth participants: (1) stretching training of muscles at risk in order to increase lengthening ability; (2) dynamic warming-up for minimizing possible imbalance between agonists and antagonists; (3) limiting practice times of the frequency and duration of movements requiring strength and/or large range of motion to reducing micro-trauma accumulation; and (4) allowing enough repair time for recovery from micro-traumas induced by training (individual training time). Collectively, the results show that biomechanical modeling is a practical tool for predicting injury risk and provides an effective way to establish an optimization strategy to counteract the factors leading to muscle repetitive stress injuries during motor skill learning and training.