AbstractPapain is widely used in food, drug, and bioactive peptide production and must be immobilized onto carriers with biocompatibility. Dialdehyde starch (DAS) can be a good biocompatible cross‐linker according to its active aldehyde groups. In the present study, the magnetic nanoparticles dialdehyde starch (MDASN), synthesized by DAS and Fe3O4 magnetic nanoparticles (Fe‐MNP), are successfully used to immobilize papain to improve the enzymic activity. The structure and morphology of DAS, MDASN, and immobilized papain onto magnetic dialdehyde starch nanoparticles (papain‐MDASN) are characterized detailly. The morphology of DAS is like a flat ball, and that of Fe‐MNP and papain‐MDASN are spherical and clumpy. The particle size of Fe‐MNP and papain‐MDASN are small, resulting in a large surface electrostatic effect and partial agglomeration. Enzymic activity studies of papain‐MDASN exhibit that the immobilized papain on MDASN represents better temperature resistance, alkaline resistance, thermal stability, and reusability, and its activity recovery is up to 68.21%. Papain onto magnetic dialdehyde starch nanoparticles (MDASN) may enhance its potential application in production processes.