Biological organisms play important roles in human health, either in a commensal or pathogenic manner. Harnessing inactivated organisms or living organisms is a promising way to treat diseases. As two types of freezing, cryoablation makes it simple to inactivate organisms that must be in a non-pathogenic state when needed, while cryopreservation is a facile way to address the problem of long-term storage challenged by living organism-based therapy. In this review, we present the latest studies of freezing biological organisms for biomedical applications. To begin with, the freezing strategies of cryoablation and cryopreservation, as well as their corresponding technical essentials, are illustrated. Besides, biomedical applications of freezing biological organisms are presented, including transplantation, tissue regeneration, anti-infection therapy, and anti-tumor therapy. The challenges and prospects of freezing living organisms for biomedical applications are well discussed. We believe that the freezing method will provide a potential direction for the standardization and commercialization of inactivated or living organism-based therapeutic systems, and promote the clinical application of organism-based therapy.