The invention relates to a process for pre-treating cotton seed, which specifically comprises cotton seed cleaning, peeling, separating kernel and shell, modifying, forming and drying so as to obtain granules. The process is characterized in that 1) after the cotton seed is cleaned and peeled, the kernel and the shell are separated; during the separation of the kernel and the shell, the shell content in the kernel is controlled at 8 to 18 percent, and the kernel content in the shell is controlled to not more than 0.5 percent; 2) during modifying, the moisture is controlled at 12 to 18 percent, preferably, 14 to 16 percent; and the temperature is controlled below 60 DEG C, preferably, 40 to 50 DEG C; 3) during forming, the barrel pressure is controlled; the temperature of the materials is controlled to not more than 90 DEG C, preferably, 70 to 85 DEG C; the oil outlet amount is controlled to not more than 16 percent; and the linearity of the formed granular material is controlled to not more than 10 millimeters; and 4) during drying, the moisture in the dried material is controlled to not more than 5 percent. The method is simple, the process is easy to control, the cotton seed protein is kept not to denature when the cotton seed is pretreated under low temperature, the cotton seed powder is little during peeling and cannot be used as a control index, and the obtained material can be directly used for grease leaching process.