The invention belongs to the field of agricultural product deep processing, and discloses a calcium pectinate production method. According to the method, raw materials are composed of agricultural and sideline product wastes or waste materials, namely citrus pericarp, lemon pericarp and imperfect fruits, shaddock peel, silkworm excrement, mangosteen peel after polyphenol is extracted, dragon fruit pomace and peel, apple pomace and peel, pineapple pomace and peel and the like, the raw materials are subjected to processes of crushing, screening, acid extracting, juice processing, neutralization, calcification flocculent precipitate, dewatering, prilling, drying and the like, and the method can be used for producing jellies, pectin, modified pectin, pectin hydrolysate, galacturonic acid and other calcium pectinate products or calcium supplement health-care food. Compared with an alcohol precipitation method, the flocculation precipitate method in the method is low in energy consumption and cost. Compared with calcium pectinate obtained through the alcohol precipitation, the calcium pectinate produced using the production method is high in biosafety degree and free of toxic and side effects.