To verify whether a low-frequency electromagnetic field (LFE field) can help reduce structural damage during the freeze–thaw process and maintain shelf life, Mongolian cheese was frozen at −10, −20, and −30 °C, then thawed at microwave or room temperature. Results showed that LFE field-assisted frozen treatment could reduce ice crystal size and protect the protein matrix structure of cheese. Frozen–thawed cheese retained 96.5% of its hardness and showed no significant difference from the fresh one in elasticity, cohesion, and chewiness. Frozen cheese showed similar but slower ripening behavior during storage, suggesting a potential application of the LFE field in the frozen storage of high-protein foods.