The invention discloses a method for extracting and separating cyclocarya paliurus flavonoids, wherein the method comprises the following steps: a, washing cyclocarya paliurus with clear water, dryingat the temperature of 40-50 DEG C, crushing the sample by a pulverizer and allowing to pass through a 40 mesh sieve; b, carrying out acidolysis; c, carrying out microbial fermentation degradation; d,carrying out compound enzymatic hydrolysis; e, carrying out acetone extraction; f, carrying out purification of crude flavonoids: purifying flavonoids with activated carbon. In the extraction processof the cyclocarya paliurus flavonoids, firstly, cell walls of cyclocarya paliurus are degraded by the preliminary microbial fermentation method, and some impurities, such as polysaccharides, are removed by microbial action; then the flavonoids are fully released by enzymatic hydrolysis. The method has no pollutant discharge in the whole technological process, is suitable for large-scale production, is beneficial to the development and utilization of cyclocarya paliurus resources, has the advantages of simple steps, low cost, strong operability and high output, and is prone to industrialized production.