The invention discloses a method for removing free gossypol in cottonseed meal through step-by-step reduction and solves the problems of low detoxification rate, high energy and water consumption and the like of conventional cottonseed meal. The technical scheme of the method comprises steps as follows: step one, cottonseed meal is smashed and then is mixed uniformly with bran and corn meal, and a mixture is taken as a substrate for standby; step two, activated bacillus and saccharomycete strains are mixed with the substrate and then subjected to solid-state fermentation, and wet based cottonseed meal is obtained; step three, the wet based cottonseed meal is subjected to microwave inactivation and detoxification and then is dried and smashed, and a finished cottonseed meal product is obtained. The method adopts a simple technology and a short detoxification process, is safe, reliable and environment-friendly and has low water and energy consumption.