MYSM1, a deubiquitinating enzyme, plays a pivotal role in diverse biological processes. Both MYSM1 knockout mice and patients with Mysm1 gene mutations exhibit developmental abnormalities across multiple tissues and organs. Serving as a crucial regulator, MYSM1 influences stem cell function, immune responses, and the pathogenesis of diverse diseases. This review comprehensively details MYSM1’s deubiquitinating activities in both the nucleus and cytoplasmic compartments, its effects on stem cell proliferation, differentiation, and immune cell function, and its involvement in cancer, aging, and depression. The high sequence homology between murine and human MYSM1, along with similar phenotypes observed in Mysm1-deficient models, provides valuable insights into the etiology of human Mysm1-deficiency syndromes. This review aims to offer a foundation for future comprehensive research on MYSM1.