The invention relates to a method for refining low-molecular-weight heparin sodium from crude protein an extractive of intimas of chitterlings. The method comprises the following steps: performing enzymolysis for prepared intestine, forming crude products, layered precipitation, ethanol sediment, crude product decomposition, competitive products forming, alcohol sediment, detergent washing and drying, wherein the ultrasonic wave is used for crude product decomposition, the raw material processing amount is large, the impurity is small, effective ingredients is easy to divorce, and the cleaning and extraction cost is low. Moreover, the comprehensive economic benefit is obvious; the ultrasonic wave has the function of cleaning and sterilization, so that the extract is not easy to spoil. In the aspects of product output rate and content, due to the adoption of the method, the heparin sodium output is improved by 20 percent as the way of enzymolysis, salting out and resin extraction is adopted, the extraction time is shortened, the running cost of the process is reduced, and the economic benefit is improved.