In recent decades, research on alternative fuel engines is becoming more and more popular. Compressed natural gas (CNG) has the advantages of abundant reserves and a lower cost. It can reduce vehicle emissions relatively quickly and has little impact on the entire transportation infrastructure. As the fourth generation of a gas fuel supply method, gas fuel direct injection (DI) technology can effectively avoid volumetric efficiency reduction and power reduction problems of the port fuel injection (PFI) method. However, the former’s mixing path and duration are shortened greatly, which often leads to poor mixing uniformity. In order to improve the in-cylinder mixing uniformity, the in-cylinder mixing process of the CNG-fueled engine is taken as the research object in this study. The computational fluid dynamics (CFDs) models of the mixing process for the PFI and DI modes are established, and their mixing uniformities are compared. Besides, based on the authors’ previous research, the influence mechanism of the piston crown shape and fuel injection angle on the mixing process of the CNG DI engine is explored. The results show that the probability distribution frequency (PDF) of the best mixture concentration region (BMCR) is as high as 72% for the PFI mode, which is much higher than for the DI mode. The shorter jet impingement distance of the flat top piston leads to higher turbulent kinetic energy (TKE) intensity, and the in-cylinder mixing uniformity will be improved. When gas fuel is injected into an area with a higher in-cylinder TKE, the average in-cylinder TKE will be higher, and the in-cylinder mixture will be more homogeneous.