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Selenium (Se) is one of the essential trace elements in animal organisms with good antioxidant and immune-enhancing abilities. In this study, we investigated the effect and mechanism of Se deficiency on skeletal muscle cell differentiation. A selenium-deficient skeletal muscle model was established. The skeletal muscle tissue and blood Se content were significantly reduced in the Se deficiency group. HE staining showed that the skeletal muscle tissue had a reduced myofiber area and nuclei and an increased myofascicular membrane with Se deficiency. The TUNEL test showed massive apoptosis of skeletal muscle cells in Se deficiency. With Se deficiency, reactive oxygen species (ROS) and malondialdehyde (MDA) increased, and the activities of glutathione peroxidase (GSH-Px), total antioxidant capacity (T-AOC), superoxide dismutase (SOD), and catalase (CAT) were inhibited. In in vitro experiments, microscopic observations showed that the low-Se group had reduced C2C12 cell fusion and a reduced number of differentiated myotubes. In addition, qPCR results showed that differentiation genes (Myog, Myod, Myh2, Myh3, and Myf5) were significantly reduced in the low Se group. Meanwhile, Western blot analysis showed that the levels of differentiation proteins (Myog, Myod, and Myhc) were significantly reduced in the low-Se group. This finding indicates that Se deficiency reduces the expression of skeletal muscle cell differentiation factors. All the above data suggest that Se deficiency can lead to oxidative stress in skeletal muscle, resulting in a reduction in the differentiation capacity of muscle cells.