A novel, magnetic three-phase fluidized bed reactor (MTFBR) was designed with magnetic immobilized cellulase (MIC) as the biocatalyst for preparing chitooligosaccharides from chitosan. The MIC showed higher enzyme activity in a pulse magnetic field (PMF) than that in a steady magnetic field (SMF) or alternating magnetic field (AMF) under certain operating parameters. The application of a magnetic field increased the maximum reaction rate (V max) and Michaelis constant (K m), and the reaction rates of the MIC-catalyzed reaction in PMF and SMF at high concentration of chitosan solution (C s, 5 < C s < 20 mg/mL) increased as the intensity of the magnetic field increased. The concentrations of chitosan pentamer and hexamer produced were higher in the PMF than in the SMF and AMF, and the application of a magnetic field greatly reduced (by as much as 37.5%) the biocatalytic reaction time required to reach the maximum concentration of the desired chitooligosaccharides. These results suggest that the customized MTFBR supplemented with MIC is a reusable and effective piece of biocatalytic equipment, indicating that it has potential applications for large industrial-scale chitooligosaccharide syntheses.