Microreactors are essential for microchemical reactions owing to their high mass transfer efficiency, precise control of reaction time, easy amplification, and good safety performance. These characteristics provide several advantages, including shortened reaction times and enhanced chemical reaction conversion rates, rendering microreactors particularly significant in chemical production. In this study, a finite-rate model was developed for the esterification of monobutyl chlorophosphate (MCP) and n-butanol in a microchannel reactor. This study investigates the impact of the microchannel’s length-to-diameter ratio, the mass ratio of n-butanol to MCP at the inlet, and the inlet flow ratio on the entire reaction system through numerical simulations. The findings indicate that increasing the length-to-diameter ratio and reducing the inlet flow rate effectively prolongs the residence time of materials in the microreactor, thereby enhancing the conversion rate of the reactants. Optimal results are achieved with a moderate n-butanol/MCP mass ratio, which facilitates MCP transformation. Moreover, this study employs response surface analysis to investigate the influence of independent factors, such as the microchannel’s length-to-diameter ratio, component ratio, and inlet velocity ratio, on MCP conversion rates. A prediction formula with conversion rate as the dependent variable and microchannel length-to-diameter ratio, component ratio, and inlet velocity ratio as independent variables was established.