The surface characteristics of carriers outstandingly influence the application of immobilized enzymes. Because of its biocompatible and multi-functional groups, chitosan was introduced into poly(styrene-co-glycidyl methacrylate) (PSt-GMA) microspheres with/ without spacer-arms. Pepsin was immobilized onto these microspheres by a simple and mild process, and then its enzymatic activity was evaluated. As for the different modified microspheres, the interactions between the carrier and enzyme molecules would be different, influencing the immobilized system. The experimental results suggested that the optimal pH for immobilized enzyme was close to the optimal reaction pH of free enzyme. It was also found that the Freundlich model fit the immobilized process better than the Langmuir model. In addition, pepsin immobilized onto chitosan modified microspheres (CMM, M3-M4) possessed a higher affinity to substrate, hemoglobin. Compared to free pepsin, the optimal reaction temperature of immobilized pepsin onto modified microspheres (M2-M4) shifted toward higher temperature. Furthermore, the thermal and storage stabilities of pepsin after immobilization were enhanced, particularly for pepsin immobilizing onto CMMs. The pepsin linked onto M3/M4 still retained approximately 70% of enzymatic activity after storing 50 days, compared to below 20% for free pepsin. In a word, CMMs provide more interactions and biocompatible surface for immobilized enzymes.