The invention relates to a method of preparing, separating and purifying 
baicalein and 
wogonin by endogenous 
enzymatic hydrolysis of 
baicalin and wogonoside in 
scutellaria, and aims at providing a simple, safe, economical and high-efficient method of extracting, separating and purifying the high-purity 
baicalein and 
wogonin. An adopted technical scheme is that the 
traditional Chinese medicine scutellaria is used as a 
raw material, a unique endogenous 
enzyme induction 
bioconversion technology, a negative-pressure 
cavitation extraction technology, a liquid-liquid extraction technique, a normal-phase silica-gel medium-and-low-pressure preparation liquid 
chromatography technology, a low-temperature 
crystallization and recrystallization technology and other high-efficient conversion, extraction, separation and purification technologies are used, and finally the high-purity 
baicalein and 
wogonin are obtained, wherein conversion rates of the 
baicalin and the wogonoside can respectively reach 98.39 % and 98.16 %, contents of the target products: baicalein and wogonin are increased by 4.47 times and 2.85 times, and a purity can be more than 98 %. The method overcomes disadvantages of large damaging effects on the 
baicalin and the wogonoside, low conversion rate and serious 
pollution existing in prior art, has advantages of simple production process, safe and 
environmental protection, high conversion rate and high target compound purity, and has a very important significance for development of medicines and health care products, and industrial production and application.