Magnetic nanocrystalline cellulose (MNCC) was prepared and used as an enzyme support for the immobilization of penicillin acylase (PA). A novel coupling agent, tri(hydroxymethyl) phosphine(THP) instead of the conventional glutaraldehyde(GA), was used as a crosslinker in this study. The obtained results showed that the immobilized PA with THP (PA-THP-MNCC) had high enzyme loading (172.3 mg/g) and activity recovery (77.6%) in the optimal preparation conditions, which were remarkably superior to those of the counterpart using GA (PA-GA-MNCC, 148.4 mg/g and 48.7%, respectively). Compared with free PA and PA-GA-MNCC, PA-THP-MNCC displayed a higher optimum pH and temperature, and manifested relatively higher enzyme-substrate affinity and catalytic efficiency. In addition, PA-THP-MNCC exhibited significantly enhanced stability. Furthermore, PA-THP-MNCC was successfully employed for synthesis of cefaclor, an important second-generation cephalosporin antibiotic, affording a significantly higher yield of 84% than that reported previously.