The disclosure herein relates to a method for preparing branched cyclodextrin and application thereof, and belongs to the technical field of synthesis of branched cyclodextrin. The method comprises the following steps: (1) dissolving maltodextrin in a phosphate buffer solution, and adding CGTase for reacting; (2) reducing enzyme activity by a physical method; and (3) adding a saccharifying enzyme to the reaction system of step (2), and performing high-temperature enzyme deactivation to obtain the branched cyclodextrin. The method has mild reaction conditions, and at the same time, cyclodextrin and unreacted substrates can be hydrolyzed via the weak coupling activity of CGTase, thereby realizing effective separation of the branched cyclodextrin.