The invention discloses a method for transforming podophyllotoxin into 4-(2,3,5,6-tetramethylpyrazine-1-group)-4'-demethylepipodophyllotoxin, comprising the following steps of: (1) adding podophyllotoxin into a liquid fermentation medium, and carrying out biotransformation by inoculating second-class liquid seeds of humic soil fungi; (2) separating and purifying the product from the Step (1), followed by adding into the liquid fermentation medium, carrying out biotransformation by inoculating second-class liquid seeds of podophyllum taxa endophytes; then continuously carrying out biotransformation by adding ligustrazine, and collecting the transformation product. The invention also discloses a method for purifying 4-(2,3,5,6-tetramethylpyrazine-1-group)-4'-demethylepipodophyllotoxin from the above product and a method for detecting the content of 4-(2,3,5,6-tetramethylpyrazine-1-group)-4'-demethylepipodophyllotoxin. According to the invention, the molecular structure of podophyllotoxin is modified by the biotransformation method, which has advantages of mild reaction condition, low E-factor, quality controllability and simple separation process.