The invention provides a polyhexamethylene guanidine propionate disinfectant and a preparation method thereof. The polyhexamethylene guanidine propionate disinfectant is a hydrophilic solution prepared by the following steps: adding polyhexamethylene guanidine propionate, citric acid and surfactant to water and uniformly stirring the mixture at normal temperature. The polyhexamethylene guanidine propionate disinfectant has the advantages of broad spectrum of disinfection, quick results, long-time disinfection capability, high safety, non-toxicity, environmental protection, high stability, easy application, quick infiltration and volatilization, no coloration, easy cleaning, and the like. The polyhexamethylene guanidine propionate disinfectant has strong sterilization functions for colon bacillus, staphylococcus aureus, candida albicans, and the like with two-year effective periods. The polyhexamethylene guanidine propionate disinfectant can be used for disinfection of skins, wound surfaces, hands, air, departments of gynecology and urology, drinking water, and the like, thereby being a novel and ideal disinfectant.