The invention relates to a method for preparing immobilized glucose isomerase with composite magnetic chitosan microballoon spheres, which comprises the steps of: adding polyethylene glycol into FeCl2 and FeCl3, dissolving, regulating pH of solution to 8 to 10 with ammonia water, washing, filtering, freezing and drying in vacuum to obtain Fe3O4 magnetic nuclei, dissolving chitosan powder in acetic acid to carry out ultrasonic dispersion to prepare chitosan solution, carrying out ultrasonic dispersion and stirring on emulsifying agents and the Fe3O4 magnetic nuclei, crosslinking 1 to 5% glutaric dialdehyde at 2000 r/min, stirring, washing, filtering, freezing and drying in vacuum to obtain composite magnetic chitosan microballoon spheres, soaking the composite magnetic chitosan microballoon spheres with phosphate buffer pH of which is 7.0 to 7.8, filtering, adding glucose isomerase diluted by buffer, vibrating, taking out the glucose isomerase, putting the glucose isomerase in a refrigerator for one night, pouring off supernate, precipitating, washing, and filtering to obtain the immobilized glucose isomerase. In the invention, the glucose isomerase activity recovery ratio of which can reach more than 80% is immobilized by the composite magnetic chitosan, and has high service efficiency, reusability and low cost.