Protein crystallization is a widely employed technique for purifying protein drugs, offering notable benefits such as cost-effectiveness and high purity. However, the success of this method is influenced by factors such as the molecular weight and spatial structure of proteins. The challenges associated with achieving crystallization and the prolonged duration required for crystallization induction pose limitations on its widespread industrial implementation. In this study, we employed lysozyme derived from egg white as a representative protein to investigate the polymer-assisted self-assembly of magnetic lysozyme. Through the optimization of the initial interstitial crystallization process of magnetic lysozyme, we manipulated the supersaturation level of lysozyme and applied magnetic nanoparticle treatment. As a result, we successfully reduced the crystallization time from 24 h to 60 min. Subsequently, the findings derived from the analysis of data pertaining to the interstitial crystallization process of lysozyme were utilized to optimize the design and configuration of a push flow crystallizer (PFC) as well as a slug flow crystallizer (SFC). The analysis encompassed the examination of various factors, including the residence time of crystallization, the yield of the process, the shape of the crystals formed, and the distribution of crystal sizes. Ultimately, it was determined that the SFC demonstrated optimal suitability for the crystallization of magnetic lysozyme. The typical V-PFC crystal size is 16 m and the yield is 60%. V-SFC crystals have an average size of 13 m and a yield of 85%.