In this study, three cylindrical combustion chambers with different diameter-to-depth ratios were designed to accelerate the flame propagation and enhance the combustion ratio of CH4 in a stoichiometric natural gas engine with exhaust gas recirculation (EGR). The effects of the diameter-to-depth ratio on the combustion and emission and the interaction between the flow field distribution and flame propagation were investigated numerically. The results showed that the value of the swirl ratio and turbulent kinetic energy (TKE) near the top dead center (TDC) could be increased continuously with a smaller diameter-to-depth ratio, which was conducive to promoting the uniform flame spread in the radial direction and enhanced the combustion efficiency. The peaks of pressure, heat release rate (HRR), and temperature dramatically increased by using the cylindrical chamber with a higher swirl ratio and higher TKE in the stoichiometric natural gas engines, thereby allowing more fuel energy to be released near the TDC in the chamber. The cylindrical chamber with the diameter-to-depth ratio of 2.36 displayed a higher peak value of combustion pressure and temperature, smaller CH4 and CO emissions, but more NOx emission, compared to other chambers. Moreover, the raised bottom bulge of the piston distorted the flame front, which accelerated the flame speed in the vertical direction. The CA50 was therefore advanced to the TDC. Thus, the cylindrical chamber with the increased squish area and the raised bottom bulge was conducive for the stoichiometric natural gas engine with EGR.