Patulin, an important contaminant in apple juice processing, exhibits various toxicities to humans. In existing patulin detoxification methods, enzymes are desirable biological detoxification agents. Here, magnetic nanocrystalline cellulose (MNCC) was prepared and employed as support for the immobilization of porcine liver esterase (PLE) to synthesize a novel cellulose-based magnetic patulin detoxification agent (PLE@MNCC). The detoxification rate of patulin by PLE@MNCC exceeded 80%. PLE@MNCC also enabled rapid separation and recovery after application while exhibiting superior storage stability, reusability and biocompatibility. After 8 repetitive cycles of usage, PLE@MNCC retained approximately 50% of its initial activity. Moreover, the cytotoxicity evaluation demonstrated a significant decrease in patulin toxicity after the detoxification. Crucially, there were no significant adverse changes in the quality of apple juice after detoxification. PLE@MNCC as an effective, reusable, environmentally friendly and safe enzyme agent provided an efficient strategy for the detoxification of patulin in fruit juices.