Abstract In the molecular layer deposition (MLD) process, the reaction chamber plays a crucial role as the deposition carrier. The geometry of the reaction chamber directly affects the deposition processes of delivery, heating of reactive gases, and purging of excessive molecules. In this study, we designed an MLD instrument for the preparation of pure organic polymer layered coatings and investigated key structural parameters of its reaction chamber. By the Computational Fluid Dynamics (CFD) method, precursor delivery, nitrogen purge, vacuuming, and oil bath heating in the deposition process were modeled. The flow field distribution under different inlet and outlet heights and the temperature field distribution under different axial heights of the chamber were analyzed, and the most suitable parameters were thus determined. The results showed that when the heights of precursor inlet, nitrogen inlet, and vacuum pumping outlet were selected as 50 mm, 45 mm, and 50 mm, respectively, the chamber could serve better deposition and purge efficiency. When the axial height of the chamber is 185 mm, both the chamber and the fluoro rubber sealing ring meet the temperature requirements.