The invention relates to a method for extracting bile salt hydrolase (BSH) of two kinds of yeasts and a production technology of functional kefir, applicable to the production of functional kefir and sour kefir in fermented dairy products. The invention adopts high-throughput screening technique and phthalic aldehyde method to acquire two kinds of yeasts which can lower cholesterol efficiently and have higher capacity of fermenting lactose, and Oxford cup method to acquire strains yielding the BSH highly through secondary screening. The invention optimizes the fermentation conditions and extraction method for the two kinds of yeasts to produce the BSH, and adopts proper cracking method by ultrasonic wave, which solves the problem that the cell walls of the yeasts are difficult to be cracked, and the cracking effect can be compared with that of the high pressure cell cracker. Kluyveromyces Marxianus K1 (CGMCC No 1812) and M3 (CGMCC No 1811) which can lower the cholesterol efficiently can yield the BSH highly and can ferment lactose to yield ethanol highly, are adopted to prepare the kefir of high quality that has the function of lowering the cholesterol. The fermentation process ofpreparing the functional kefir is simple with shorter fermentation period and lower cost. Thus, the fermentation process is applicable to mass industrial production.