The invention discloses a method for preparing a compound enzyme and probiotic preparation for feed through the biotransformation of broad bean stems / leaves and cottonseed meals. The method comprises the steps of: thoroughly mixing cooked Pu'er tea, mushroom sticks, tea tree mushroom sticks, first broad bean stems / leaves, first cottonseed meals, first wheat bran, first apple pomace and first water which are subjected to pile fermentation, and carrying out acclimation culture so as to form a leavening agent; and thoroughly mixing the leavening agent, second broad bean stems / leaves, second cottonseed meals, second wheat bran, second apple pomace and second water, and carrying out fermentation, thereby obtaining the compound enzyme and probiotic preparation for feed. According to the method, the compound enzyme and probiotic preparation with better various performance indexes is prepared through fermenting the broad bean stems / leaves and the cottonseed meals by using food-grade safe flora with stable microbial states, so that the low-cost and high-efficiency biotransformation of the broad bean stems / leaves and the cottonseed meals is realized. Meanwhile, the method disclosed by the invention has the advantages that microbes grow easily, the enzyme activity is high, the fermentation process is extensive, and the industrial large-scale production is facilitated.