Carboxymethyl chitosan (CMC)-based hydrogels have great potential for clinical applications, but a critical sterilization process must be addressed to bring them to market. Compared to ethylene oxide sterilization or heat sterilization, irradiation sterilization avoids alkylation and heat damage, while available studies on γ-irradiated other polysaccharides show that solution polysaccharides are susceptible to degradation or cross-linking. Aiming at the challenges brought by the γ-irradiation process of polysaccharide aqueous solution, this paper innovatively proposes the lyophilized CMC using electron beam (EB) irradiation, which not only avoids the generation of free radicals in the irradiated water leading to the degradation and cross-linking of polysaccharides but also retains the properties of CMC in terms of gel formation, stabilization, and clinical application. We used FTIR, TG, GPC, and microbial load tests to demonstrate that lyophilized CMC did not have significant changes in structure and molecular weight after EB irradiation, complied with the requirements for sterilization, and still had gel stability, thus proving that lyophilized CMC could be used for EB irradiation and met the requirements for clinical application. Therefore, this work is expected to further advance CMC injectable hydrogels toward clinical applications and provide a new direction for the sterilization processes of other polysaccharide hydrogels.