The invention discloses a method for converting echinomycin B by an immobilized microbial enzyme, and belongs to the field of bioengineering. The method comprises the following steps: (1), fermentingactinoplanesutahensis, collecting mycelia, disrupting cells through ultrasonic disruption by using a cell disrupting device, centrifuging, taking a supernatant to obtain a crude enzyme solution of echinomycin B deacylase; (2), slowly adding an ammonium sulfate solution into the crude enzyme solution in the step (1) to obtain a precipitate; (3), dissolving the precipitate in the step (2) in a buffered salt solution; (4), adding odium alginate into the solution in the step (3), stirring uniformly, then dropwise adding a pre-cooled aqueous calcium chloride solution, placing in a refrigerator overnight, and filtering to obtain the immobilized microbial enzyme; and (5), dissolving echinomycin B in ethanol, and adding the immobilized microbial enzyme in the step (4), converting, and collecting afiltrate to obtain an echinocandin B mother nucleus solution. By the method, the conversion rate is high, the conversion time is short, a product is easy to separate, a conversion solution contains less pigments, and the immobilized enzyme is easy to store and can be reused.