The present invention belongs to the technical field of food and particularly discloses gel encapsulated hippocampal polypeptide microcapsules and a preparation method thereof. The microcapsules are mainly composed of the following ingredients in weight: 6-8 g of soy protein isolate, 2-4 g of peanut protein isolate, 2-3 g of Arabic gums, 80-86 g of water, 3 g of a sweetener, 0.1 g of a preservative and 1-1.5 g of hippocampal polypeptides. Due to the fact that the plant protein itself is relatively high in nutritional value and good in embedding properties, the utilized plant protein gel embedding method is the active substance embedding technology which is green, healthy and effective. Besides, the peanut proteins are used to replace parts of the soybean proteins, so that the color of the finished products is refresher and the smell of the beans can be effectively covered. In addition, the constructed Arabic gum-soybean-peanut protein mixed gel can effectively improve the embedding effects of the mixed gel and stabilize the bioactivity of the hippocampal polypeptides.