The invention discloses a method for preparing chondroitin sulfate. The method comprises the following steps: adding water to immerse cartilage, adjusting the pH value to be 8-9 with alkali, and carrying out heat preservation at 55-60 DEG for 4-6 hours; adding 2709 alkaline protease, stirring for 6-8 hours, heating until boiling, and filtering to obtain chondroitin sulfate liquid; adding sodium chloride to the chondroitin sulfate liquid, adding ethyl alcohol which is 2-3 times of volume of the liquid, standing for 6 hours, and filtering to obtain chondroitin sulfate sediments; adding water to the chondroitin sulfate sediments for dissolving, simultaneously adding sodium chloride to water, and adjusting pH value to be 10-12; adding hydrogen peroxide which is 1%-3% of weight of the liquid, oxidizing for 6 hours, and filtering to obtain filtrate; adjusting the pH value of the chondroitin sulfate filtrate to 5-6, adding ethyl alcohol which is 4-6 times of volume of the filtrate, and participating for the second time, so as to obtain chondroitin sulfate sediments; pouring the chondroitin sulfate sediments into a dewatering tank with an emulsifier; pumping ethyl alcohol which is 3-5 times of volume of the chondroitin sulfate sediments into the dewatering tank, carrying out suction filtration, collecting sediments, and drying to obtain a chondroitin sulfate product. The chondroitin sulfate obtained by the method is loose in texture, small in particles, easy to dewater and dry, low in energy consumption, very low in organic solvent residue and short in production cycle.