The invention provides a method for extracting, separating and purifying formononetin and calycosin from Astragalus mongholicus waste residue. The technical scheme adopted in the invention is as follows: taking waste residue after the production and process of astragalus injection as a raw material; adopting a series of original and efficient technologies for extracting, separation and purifying such as homogenate extraction-mixing enzyme induction biotransformation technology, negative pressure cavitation extract technology, liquid-liquid extraction technology, macroporous absorption resin enrichment technology, normal phase silica gel medium pressure column chromatography technology and devitrification at a low temperature, recrystallization technology and the like to obtain the formononetin and calycosin with high purity, wherein the purity thereof can be more than 95%, and the yield is 80-95%. The raw material used in the invention is the waste residue in the industry production, and the process of the method is simple and practicable, has small pollution to the environment; the obtained formononetin and calycosin have low production cost, high purity and yield, good repeatability, high utilization effect of Astragalus mongholicus resources and the like; and the method is suitable to scaled industrial production.