The development of novel approaches for preparing the immobilized enzyme reactors with improved reusability and catalytic performance has attracted tremendous interest because of the extensive applications and the high cost of free enzymes. Herein, we describe a mild and versatile method for the preparation of immobilized enzyme reactors by anchoring trypsin on polydopamine (PDA) functionalized magnetic nanoparticles (MNPs) through DNA directed immobilization (DDI). This reactor exhibited prominent reusability and enhanced catalytic efficiency. The specificity constant (kcat/Km, where kcat is the catalytic rate constant) of the reactor was 1.82 s−1 μM−1, which was approximately 4.7-fold higher than free trypsin. Notably, the immobilized trypsin reactors maintained more than 55% of their initial activity after 70 cycles (in pH 9.0 PBS, 37 °C). The improved activity and reusability were dually benefited from the rigidity and stability of DNA linkers as well as the excellent biocompatibility and cushioning effects of PDA. Given the excellent reusability and high catalytic efficiency of this immobilized trypsin reactors, we believe that this study paves the way for preparing low-cost enzyme reactors for a wide range of applications in biocatalysis, biological diagnosis, and biotechnology.