In the experiments, the extraction of the fish scale collagen with pepsin under the acid condition, concerning with three factors: E/S, fish scales protein concentration and extraction time in a mixed uniform design or a orthogonal design was studied. Finally the best condition of extraction with pepsin was determined: 30 mg pepsin to 1 g fish scale, 3 % acetic acid 80 mL, shaking at the constant temperature (18 ℃) for 48 h.