The invention provides a method for extracting protein from cottonseed meal. The method comprises the following steps: a, adding water and mixing after smashing the cottonseed meal, and carrying out centrifugal separation; b, filtering a solution, removing residues, then carrying out alkali dissolution, adding protease, heating, and keeping the temperature be 40 to 50 DEG C, the pH (Potential of Hydrogen) value of the solution be 7.5 to 8.0 and the heating time be 3 to 5 hours; c, quickly rising the temperature to 80 to 90 DEG C, and stopping heating after carrying out sterilization and enzyme deactivation treatment; d, then adding sodium chloride in the solution, and concentrating and drying the solution after uniformly stirring, thus obtaining the protein in the cottonseed meal. According to the method provided by the invention, the resource is fully utilized, the protein which is high in nutritive value in the cottonseed meal is extracted, the extracted protein is high in purity and few in impurities and has no residue of an industrial extraction additive, a preparation technology is simple, the cost is low, but the value is high, and the method is suitable for industrial large-scale production.