The invention discloses a process for preparing heparin sodium through membrane separation. The process comprises the steps: intestinal mucosa enzymolysis, ceramic membrane filtration, ion exchange column chromatography, nanofiltraiton membrane concentration, alcohol precipitation and drying, wherein the optimal condition for the intestinal mucosa enzymolysis is formed by the proper proportion of intestinal mucosa to water, enzymolysis temperature and pH value of a system. A protease can take the optimal enzymolysis effect, the structure and activity of heparin are not damaged when the glucosidic bond linked between protein and the heparin is hydrolyzed, meanwhile, fewer low-molecular heparins are generated, the activity of the heparin can be improved by 20%, and the generated low-molecular heparins can be reduced by 10%. Due to the adoption of the ceramic membrane filtration, protein impurities and the heparin in an enzymatic hydrolysate can be effectively separated, so that the heparin loss is greatly reduced and can be reduced by 5-8% as comparison with that of the traditional process, the production cost is reduced, the discharged wastewater can be reduced by 50-60%, the resin utilization ratio can be increased by 40-50%, the consumption of auxiliary materials is low, the quality of the heparin sodium is stable, the process is convenient to operate, and the defects such as high impurity content in the enzymatic hydrolysate, serious waste liquid discharge pollution, high personnel utilization rate and the like are overcome.