Thrombus-related diseases have a high mortality rate and are seriously threatening human life and health. Nattokinase (NK), which has a strong thrombolytic effect, can treat thrombotic diseases. In this study, NK-conjugated magnetite nanoparticles (NK-MNPs) were prepared to accurately deliver NK to the thrombus site. Fe₃ O₄, carboxymethyl chitosan and sodium alginate were combined to form magnetite nanoparticles (MNPs), which were prepared to encapsulate NK. The mean diameter of NK-MNPs was 168.9±4.8 nm, and the zeta potential was -33.8±0.9 mV. The release percentage reached a plateau in approximately 12 h, with 65.24% NK released. Magnetic targeting experiments showed that the light transmittance of the solution reached 90%. The results from the in vitro thrombolysis experiments demonstrated the sustained release thrombolysis potential of NK-MNPs. A hemolysis experiment demonstrated that the hemolysis rate of NK-MNPs was less than 5% at an enzymatic activity of 50-150 IU/mL. Moreover NK-MNPs were stored for 90 days at 4 °C and still maintained an enzyme activity above 90%. In conclusion, NK-MNPs hold great promise for improved thrombolytic efficacy, with sustained release and magnetic targeting.