The invention relates to a method for extracting branched chain amino acid from fermentation liquid by virtue of a double-membrane continuous crystallization method. According to the method, thalluses, most protein and pigments in the fermentation liquid are filtered in a cross flow manner by virtue of a double-membrane (micro-filtration membrane and nanofiltration membrane) separation system, then operation steps including sol deproteinization, activated carbon decoloration, vacuum concentration and crystallization, alkali dissolution, deproteinization decoloration, low-temperature iso-electric continuous crystallization and the like are carried out so as to obtain branched chain amino acid crystals with the purity not less than 98.5%, and the yield is not less than 80%; the thalluses are filtered by virtue of the micro-filtration membrane, and methods including centrifugation, filter press filter pressing and the like adopted in conventional fermentation liquid treatment are changed, so that the thalluses are thoroughly removed, and filtrate is clear and transparent; soluble protein in the fermentation liquid is further removed by virtue of sol, and a low-temperature iso-electric continuous crystallization manner is adopted, so that the product quality is improved; a traditional ion exchange process is omitted, so that the production of a lot of high ammonia-nitrogen wastewater is avoided, and the clean production of branched chain amino acid is realized.