The SiO2-coated Fe3O4 composite particles (Fe3O4@SiO2) were prepared, and modified with 3-aminopropyltriethoxysilane (APTES) to prepared aminosilane functionalized magnetic materials (Fe3O4@SiO2-NH2), which were used as carriers for immobilized agarase to produce agarose oligosaccharides. SEM and FTIR characterization results proved that agarase was successfully immobilized on the carrier; VSM characterization results showed that magnetic saturation intensity of Fe3O4@SiO2-NH2 was 48.4 emu/g, and the magnetic saturation intensity of immobilized agarase was 42.8 emu/g, both of them had high magnetic properties. By optimizing the enzyme immobilization conditions, the enzyme activity recovery was 67.74% under the conditions of 7mL enzyme addition,4mL glutaraldehyde addition,2h cross-linking time and 2h immobilization time. Compared with the free agarase, the immobilized agarase had stronger thermal stability and pH stability; moreover, the relative activity of immobilized agarase was 40.41% after 7 applications.