This study examines boundary layer control and pressure recovery in low Reynolds number supersonic flow with chemical reactions in a chemical laser system. Our work prescribes a novel boundary layer control method for the optical cavity of a chemical laser system, and a design of a supersonic diffuser is compared and proposed to make a stable flow for the system. The flow characteristics of a low Reynolds number and internal reaction heat release were analyzed. Three types of experimental pieces were designed to passively control the boundary layer in the optical cavity. An active booster-type supersonic diffuser is proposed to study the pressure recovery problem of a low Reynolds number and chemical reaction supersonic flow generated by an optical cavity. A supersonic chemical reaction platform (SCRP) was established to conduct experimental research on boundary layer control and docking the active booster supersonic diffuser with the SCRP. The experimental results indicate that increasing the boundary layer pumping capacity within a certain range can reduce both the boundary layer thickness and the pressure on the optical cavity while simultaneously enhancing the SCRP energy power. The supersonic diffuser based on active gas pressurization can create the necessary conditions for the normal chemical reaction and improve the ability of the SCRP to resist high back pressure and airflow disturbance. Moreover, the chemical reaction energy release was full and stable with the docking of supersonic diffuser test pieces, resulting in energy power increases, which could be a significant improvement for the design of chemical laser systems.