Abstract: Currently, agricultural diesel engines are predominantly equipped with traditional inclusive combustion systems based on the ω (omega) combustion system. These systems have relatively low combustion levels inside the cylinder, leading to increased fuel consumption and higher carbon soot emissions. This issue becomes even more pronounced in high-altitude environments where oxygen levels are low. This study aims to address the performance optimization of high-altitude agricultural engines under such specific conditions, providing crucial insights into improving fuel efficiency and reducing emissions. The study utilizes AVL Fire software to establish a wall-flow-type TCD (turbocharger, charge air cooling, diesel particle filter) combustion system model. The primary goal is to investigate the impact of the VIA (vertical injection angle), on the combustion and emission performance of the system under different load conditions. The research explores how VIA affects the fuel-air mixture characteristics inside the cylinder in high-altitude conditions. Additionally, the study analyzes the VIA matching rules under various load conditions and proposes a VIA matching strategy for optimizing the TCD combustion system of high-altitude agricultural diesel engines. The results from the study can be summarized as follows: 1) Under high-altitude conditions and at high load working conditions (100% and 75%), when the VIA is too large, the combustion performance of the TCD combustion system declines gradually. However, when the VIA is too small, the combustion performance sharply decreases. After the fuel injection ends, a large amount of mixed fuel accumulates in the bottom arc and central region of the combustion chamber, resulting in poor combustion efficiency. 2) For medium and low load conditions (50% and 25%), when the VIA is too small, combustion performance declines slowly over time. In contrast, when the VIA is too large, the combustion performance deteriorates rapidly. After injection ends, the mixed fuel accumulates near the cylinder head region of the combustion chamber, leading to a highly localized, inefficient burn. 3) The study determined the optimal fuel jet angles for the TCD combustion system at various load conditions, specifically at 100%, 75%, 50%, and 25%. The vertical injection angles were found to be 143°, 144°, 146°, and 146°, respectively. As the load increases, the optimal VIA angle gradually decreases. This indicates that the combustion system becomes more sensitive to VIA changes as the engine load increases. 4) For the design of the VIA in high-altitude agricultural diesel engines' TCD combustion systems, it was found that using a high-load condition (75%) for matching provides the best overall performance across different load conditions. 5) Experimental verification of the VIA matching for the TCD combustion system demonstrated significant improvements in combustion performance. The spray collided with the annular protrusion structure on the wall, creating a vortex flow that facilitated better mixing of the fuel and air. As a result, the combustion efficiency of the system was significantly improved when compared to the original ω combustion system. Specifically, the effective fuel consumption rate decreased by 7.2–12.8 g/(kW·h), and the smoke opacity was reduced by 60%–91% under load conditions ranging from 25% to 100%. The findings from this research provide a comprehensive understanding of the relationship between VIA and combustion performance in high-altitude agricultural diesel engines. By optimizing VIA, this study offers valuable theoretical support and technical references that can be applied to the design and performance optimization of engines operating in high-altitude environments. These improvements not only enhance fuel efficiency but also contribute to the reduction of harmful emissions, making the engines more environmentally friendly and economically viable for agricultural use in challenging high-altitude regions. The study's results will aid in the development of future engine technologies that are better suited to operating under extreme atmospheric conditions.