To improve the catalysis of pullulanase from Anoxybacillus sp.WB42, Fe3O4@polydopamine nanoparticles (Fe3O4@PDA) were prepared and modified with functional groups for immobilization of pullulanases via covalent binding or ionic adsorption. Immobilized pullulanases had lower thermal stability than that of free pullulanase, whereas their catalysis depended on the surface characteristics of nanoparticles. As for covalent immobilization of pullulanases onto Fe3O4@PDA derivatives, the spacer grafted onto Fe3O4@PDA made the catalytic efficiency of pullulanase increase up to the equivalence of free enzyme but dramatically reduced the pullulanase thermostability. In contrast, pullulanases bounded ionically to Fe3O4@PDA derivatives had higher activity recovery and catalytic efficiency, and their catalytic behaviors varied with the modifier grafted onto Fe3O4@PDA. Among these immobilized pullulanases, ionic adsorption of pullulanase on Fe3O4@PDA-polyethyleneimine-glycidyltrimethylammonium gave a high-performance and durable catalyst, which displayed not only 1.5-fold increase in catalytic efficiency compared to free enzyme but also a significant improvement in operation stability with a half of initial activity after 27 consecutive cycles with a total reaction time of 13.5 h, and was reversible, making this nanoparticle reusable for immobilization.