In order to enhance the efficiency of diphenyldimethoxysilane preparation in microreactors, this study utilized the computational fluid dynamics simulation based on the finite element method to explore the impact of the internal structural parameters of the spiral two-step microreactor (STMR) on the reaction outcomes, with the aim of optimizing its structure for high-performance catalytic reactions. By designing a microreactor based on the Archimedean spiral shape and introducing two ribbed obstacles, the structure was optimized through adjusting the relevant ratios. The effects of different-sized structures and obstacles within the reaction zone and non-reaction zone on the product concentration and reaction results were discussed. The results demonstrate that lower obstacle heights and smaller aspect ratios (P = 2:7, R = 5:6) are beneficial for improving the reaction efficiency and product concentration. This study offers a theoretical foundation for microreactor design and is anticipated to further drive the development of microreactor technology.