Mucor irregularis poses significant clinical risks, including severe disfigurement, with hyphal forms being more commonly encountered in clinical settings compared to spore forms. However, the pathogenic differences between these forms at the protein level remain poorly understood. This study employed TMT-based quantitative proteomics to investigate the proteomic differences between spores and hyphae of Mucor irregularis. Our analysis revealed that differentially abundant proteins are predominantly expressed during the hyphal stage. Notably, key enzymes such as RhoGEF GTPase, Subtilisin-related Protease, Acyl-CoA Synthetase, and Ribonuclease T2 appear crucial for hyphal morphological development and pathogenic mechanisms. Additionally, myosins play a significant role not only in hyphal growth and virulence but also in influencing sensitivity to antifungal agents. These findings provide new insights into the morphogenesis, development, and metabolic processes of Mucor irregularis, laying a foundation for further research into its pathogenic mechanisms.