Objective To explore the optimal method for preparing fresh and fixed skeletal muscle tissues, and to lay an experimental foundation for the rapid diagnosis of and research into the pathogenesis of skeletal muscle diseases. Methods The tibialis anterior muscle was extracted from C57BL/6J mice. Fresh tissue was treated by direct rapid freezing in liquid nitrogen, embedding combined with liquid nitrogen freezing, and foreign body alkane treatment combined with liquid nitrogen freezing. Fixed tissues were pre-treated by direct embedding with embedding agent combined with rapid liquid nitrogen freezing. The frozen sections were stained with hematoxylin and eosin. The cross-sectional areas of ice crystals and muscle fibers were calculated to evaluate the effects of the different pre-treatment method. Results The morphology of the muscle fiber bundles was disrupted and numerous ice crystal vacuoles were observed in fresh tissues after direct liquid nitrogen freezing and foreign body alkane treatment combined with liquid nitrogen freezing. In contrast, the muscle fiber bundles were intact and dense and there were no ice crystals in tissues treated with embedding agent combined with rapid liquid nitrogen freezing, indicating that this pre-treatment method was suitable for preparing fresh skeletal muscle tissue. Fixed tissue treated with embedding agent and liquid nitrogen freezing also showed complete muscle fiber bundles and no ice crystals. Conclusions Treatment of fresh and fixed skeletal muscle tissues with embedding agent combined with rapid liquid nitrogen freezing preserves muscle fiber bundles, with no ice crystals. Tissues prepared by this method are thus suitable for further examinations, such as immunohistochemistry and immunofluorescence. This method will therefore aid the accurate and rapid diagnosis of and research into the pathogenesis of skeletal muscle diseases.