The invention specifically relates to a method for recovering a protein from heparin sodium extraction waste liquid, which comprises the following steps: adding an aluminum salt solution in heparin sodium extraction waste liquid, and stirring; after uniformly stirring, adding a flocculant solution, and stirring; when a large amount of flocculent precipitate appears, standing; drawing off the supernatant, and collecting the precipitate; and drying to obtain the protein. According to the invention, the used polyaluminum chloride product has high bridging adsorbability, and physical and chemical processes such as condensation, adsorption, precipitation and the like are accompanied in the hydrolytic process. The polyaluminum chloride structurally comprises a shape-variable multi-element carboxyl complex, has a high flocculent precipitation speed and a wide applicable pH value range, and causes no corrosion to pipeline equipment. The high molecular weight polyacrylamide forms bridges among the adsorbed particles to generate flocs, thereby being beneficial to settling of the particles; and the polyacrylamide is low in consumption, high in efficiency and easy to realize post treatment.