With the increasingly stringent mandatory emission regulations for engines and the continuous growth of energy consumption, reducing energy consumption and emission pollution has become an inevitable choice for engine development. Against this backdrop, biodiesel and boot-shaped injection rates have attracted widespread attention. However, research results on the combination of boot-shaped injection and biodiesel applied to engines have not yet been reported. In order to provide direction for the optimal matching of the combustion system parameters of biodiesel engines under saddle-shaped injection conditions, this paper achieves boot-shaped injection using a dual solenoid valve control strategy for ultra-high-pressure fuel injection devices, establishes a simulation model of biodiesel engines under saddle-shaped injection conditions using software and validates the model based on experiments. Subsequently, the model is used to study the influence of nozzle numbers, swirl ratio and bore-to-stroke ratio on the performance of biodiesel engines under saddle-shaped injection conditions. The results show that under saddle-shaped injection conditions, appropriately increasing the nozzle hole can refine the fuel spray, which is beneficial for fuel–air mixing and combustion in the cylinder. However, too many nozzle holes can lead to interference between adjacent fuel sprays. When the swirl ratio is large, air flow accelerates, and the oxygen concentration in the cylinder increases, which can effectively control soot formation. When the bore-to-stroke ratio is large, the fuel spray is farther away from the combustion chamber side wall, facilitating sufficient contact between fuel and air, resulting in better fuel–air mixing and effectively reducing soot formation. However, the cylinder temperature also increases, leading to higher NOx formation.