The invention discloses a method for evaluating a fish intestinal tract tissue slice, and belongs to the field of aquatic products. The method comprises the following steps: observing a mucous membrane layer, a submucous membrane layer, a muscular layer and a serosa layer of a target tissue slice by using a microscope, and respectively scoring observed symptom results; wherein the weights of the mucous membrane layer, the submucous membrane layer, the muscular layer and the serous membrane layer are b1, b2, b3 and b4 respectively, b1 is larger than b2, b3 is larger than b4, and b1 + b2 + b3 +b4 = 1; score of intestinal tissue slices. According to the invention, a weighted scoring method is adopted, an intestinal tissue pathological symptom index scoring standard is established, comprehensive quantitative evaluation is carried out on the intestinal tract tissue slices. The weight of different symptoms of the same structural layer and the weight of different structural layers of intestinal tissues are determined according to the importance degree, finally, the grade score of each symptom is multiplied by the symptom weight to obtain the score of each structural layer, all symptoms of each intestinal slice are comprehensively considered and finally converted into data for statistical analysis, and the data is objective and comprehensive.