A fully three-dimensional model was used to investigate the optimal value for intake valve lift in a CAI engine. Uniform mixing in the engine is a key parameter that affects the auto-ignition reliability and thermal efficiency. The method of intake of the air supply often determines the uniformity (or quality) of the fuel-air mixture. In this paper, four strategies were applied for controlling the swirl intensity of intake air. The variation of the intake valve lift induces different swirling and tumbling intensities. Both experimental data and 1D WAVE software (Ricardo, Co.) were coupled with the 3D model to provide pressure and temperature boundary conditions. The initial condition of the EGR mass fraction was also provided by the 1D model. The benchmark scenario (Case 1) was considered as a valve lift with 2 mm for all intake valves. We found that an intake valve lift of 6 mm with the other intake valve closed (i.e., Case 5) yielded the largest swirling (helical motion in the axial direction) and tumbling, which in turn rendered optimal fuel-gas mixing. We also found that fuel distribution affected the auto-ignition sites (or spot). The better the mixing, the greater the gas temperature and combustion efficiency achieved, as seen in Case 5. The NOx level, however, was increased due to the gas temperature. The optimal operating condition is selected from the viewpoints of environmental protection and combustion efficiency.