Due to the recent global increase in fuel prices, to reduce emissions from ground transportation and improve urban air quality, it is necessary to improve fuel efficiency and reduce emissions. Water, methanol, and a mixture of the two were added at the pre-intercooler position to keep the same charge and cooling of the original rich mixture, reduce BSFC and increase ITE, and promote combustion. The methanol/water mixing volume ratios of different fuel injection strategies were compared to find the best balance between fuel consumption, performance, and emission trends. By simulating the combustion mechanism of methanol, water, and diesel mixed through the Chemkin system, the ignition delay, temperature change, and the generation rate of the hydroxyl group (−OH) in the reaction process were analyzed. Furthermore, the performance and emission of the engine were analyzed in combination with the actual experiment process. This paper studied the application of different concentration ratios of the water−methanol−diesel mixture in engines. Five concentration ratios of water−methanol blending were injected into the engine at different injection ratios at the pre-intercooler position, such as 100% methanol, 90% methanol/10% water, 60% methanol/40% water, 30% methanol/70% water, 100% water was used. With different volume ratios of premixes, the combustion rate and combustion efficiency were affected by droplet extinguishment, flashing, or explosion, resulting in changes in combustion temperature and affecting engine performance and emissions. In this article, the injection carryout at the pre-intercooler position of the intake port indicated thermal efficiency increase and a brake specific fuel consumption rate decrease with the increase of water−methanol concentration, and reduce CO, UHC, and nitrogen oxide emissions. In particular, when 60% methanol and 40% water were added, it was found that the ignition delay was the shortest and the cylinder pressure was the largest, but the heat release rate was indeed the lowest.