In this work, novel silica hybrid magnetic particles with biocompatible surface were designed as a support for enzyme immobilization, and the immobilized chymotrypsin (CT) performance was clarified as a model biocatalyst. CT is used in food technology for drink clarification and protein hydrolysis. The enzyme was directly immobilized onto polydopamine-grafted magnetic silica particles (MNP@SiO2@PDA-CT) via the Schiff base reaction. Immobilized enzyme had broadened for both pH and temperature profiles compared with the native CT. The MNP@SiO2@PDA-CT system also improved in thermostability compared with the native enzyme. The immobilized CT was operated in a continuous enzyme reactor (CER) for the hydrolysis of different proteins (i.e., cytochrome c (Cyt c), human serum albumin (HSA), human immunoglobulin G (HIgG), and lysozyme (Lys)). The peptide synthesis rate was shown to decrease as a function of increasing flow rate. The catalytic activity of the CER remained stable for 6.0 h in a continuous operation period; thus, the presented method may increase applicability in the food technology area. The immobilized CT in the CER showed a good hydrolysis performance for all the tested model proteins. The peptides hydrolyzed from the tested proteins were analyzed with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF-MS). Results show that the MNP@SiO2@PDA-CT system also permits for the applicability in the area of proteomic research.