The invention discloses a microbial enzymatic conversion method for echinocandin B, and particularly relates to a method of converting the echinocandin B into an echinocandin B nucleus. The method includes performing microbial fermentation to produce echinocandin B deacylase, extracting to obtain crude enzyme, and converting through adding the crude enzyme and the echinocandin B in a batch manner. The method is high in mole conversion ratio, high in product concentration, and beneficial to separation and purification. An echinocandin B substrate can be recovered and reutilized, thus reducing a production cost.