The application discloses a water-treated polyhexamethylene guanidine hydrochloride sterilizing agent and a preparation method thereof. The water-treated polyhexamethylene guanidine hydrochloride sterilizing agent is prepared by weighing and uniformly mixing guanidine hydrochloride, hexamethylene diamine, hexamethylenediamine, polyethylene glycol, water, methylbenzene, a polymerization inhibitor, sulphonic acid, maleic anhydride, N-t-butyloxycarboryl-1,6-diamino hexane, a dispersing agent, ferric sulfate, methacrylic acid, dodecyl dimethyl benzyl ammonium chloride and methyl acrylate according to parts by weight. The water-treated polyhexamethylene guanidine hydrochloride sterilizing agent is 100% soluble in water, has no volatility, can be completely neutralized with soaps, and has no pollution to environment; the integral of an acute skin irritancy test is 0, and the water-treated polyhexamethylene guanidine hydrochloride sterilizing agent is colorless, non-poisonous, odorless and tasteless, and has no corrosion to metal, rubber and plastic; the sterilizing rate to escherichia coli, staphylococcus aureus, candida albicans, neisseria gonorrhoeae, penicillium, aspergillus, saprophytic bacteria and salmonella is 100%, when the water-treated polyhexamethylene guanidine hydrochloride sterilizing agent is placed at 50-60 DEG C for a month, the sterilizing rate is 98-100%, when the water-treated polyhexamethylene guanidine hydrochloride sterilizing agent is placed at 40-50 DEG C for half a year, the sterilizing rate is 97.5-99.5%, and when the water-treated polyhexamethylene guanidine hydrochloride sterilizing agent is placed at the room temperature for 1-2 years, the sterilizing rate is 95-99%.