Abstract: The high-altitude areas in China are vast, with regions above 2000 meters accounting for more than 30% of the country's total land area. The inherent low-oxygen content of the high-altitude environment results in insufficient uniformity of the fuel-air mixture in the diesel engine cylinder, thereby degrading combustion performance. Currently, most diesel engines used in agricultural applications in high-altitude areas employ smaller cylinder diameters and encompassing combustion systems. However, the diesel engine's injection pressure is constantly increasing to meet market demands, resulting in the inevitable occurrence of the "wet wall" phenomenon in the diesel engine cylinder, which is not conducive to the release of the combustion performance of small-cylinder-diameter agricultural diesel engines. This study aims to improve the combustion performance of agricultural diesel engines operating at high altitudes by introducing the lateral swirl combustion system (LSCS). Based on the prototype ω combustion system (OMCS), the LSCS was modified for the diesel engine combustion chamber. Using the CFD software AVL Fire, the combustion and emission characteristics of LSCS at 1800 and 3600 r/min under load conditions of 100%, 75%, 50%, 25%, and 15% were analyzed. The improvement rules of LSCS for the combustion and emission characteristics of agricultural diesel engines in high-altitude areas were summarized, and the mechanism by which LSCS improves cylinder fuel-air mixture characteristics was analyzed in depth. The results show that in the entire load range at both rotational speeds, the combustion performance of LSCS is improved compared to OMCS. Specifically, at 1800 r/min and 3600 r/min, the application of LSCS reduces the indicated specific fuel consumption (ISFC) by 3.41–14.85 g/kW·h and 3.34–11.84 g/kW·h, respectively, and reduces particulate emissions by 6.84%–21.04% and 12.68%–39.59%. It is noteworthy that in the medium- and low-load ranges, the application of LSCS has a more significant improvement in the combustion performance of the diesel engine. Through mechanistic analysis of fuel-air mixture characteristics, it was found that, due to the longer fuel injection duration under heavy-load conditions, the split-flow convex-edge structure of the LSCS can fully exert its functions of wall-flow guidance and wall-jet interference on the fuel. The resulting lateral swirl promotes fuel diffusion near the split arc and within the wall-jet interference zone. At this time, the LSCS in the cylinder shows relatively excellent uniformity of fuel-air mixture. Meanwhile, the OMCS at this time can also form wall jets adhering to the cylinder wall by means of the annular bulge and wall curvature, to some extent, playing a role similar to that of the swirl combustion system in guiding the fuel flow on the wall surface, improving the utilization rate of air and space in the cylinder. Based on the above reasons, under heavy-load conditions, the LSCS improves the combustion performance of the diesel engine, but the improvement is not significant. Under medium- and low-load conditions with shorter fuel injection durations, the split-flow structure of the LSCS can still exert a certain wall-flow-guiding effect, and more fuel is discharged from the cylinder wall, thereby avoiding the "wet wall" phenomenon. However, since the OMCS lacks a wall-flow guiding structure, the fuel cannot be effectively discharged from the wall or diffuse effectively after hitting it; more fuel remains on the cylinder wall. Due to the energy attenuation during the movement, more fuel accumulation areas appear in the cylinder, which is not conducive to the suction of air by the fuel in the cylinder, deteriorating the fuel-air mixture characteristics, and ultimately leading to a significant improvement in the combustion performance of the LSCS compared to the OMCS in the low-load conditions. These findings provide a reference for the application of wall-guided combustion systems in high-altitude regions.