Recently, the shortage of fossil resources contributes to strict regulations of environmental protection. The research on the high efficiency and low emission of engines becomes an important direction all over the world. Technologies like high injection pressure, high levels of supercharging and higher levels of back pressure have come into application. Increasing the injection pressure and average cylinder pressure results in that parts of the spray can experience transcritical and supercritical regimes. In this paper, we established a surrogate fuel composed of n-Hexadecane, HMN and 1-Metylnaphthalene, to analyze the injection and atomization of diesel surrogate fuel with large eddy simulation (LES) in a cubic calculation region with high temperature and high pressure environment. The injection pressure was fixed to 150MPa, and the 900-K temperature and the 6-MPa pressure represented the ambient condition in constant volume vessel which is supercritical with respect to No.2 diesel. Analyses of No.2 diesel and the surrogate fuel were performed to compare the characteristics of injection and atomization. To illustrate the differences, liquid penetration, jet penetration and spray cone angle of these two fuels were studied and discussed, and the influencing factors like distillation temperature, kinematic viscosity and density were considered as important reasons. The result shows that when the surrogate fuel is injected into the ambient under supercritical conditions, the liquid penetration is slightly longer than that of No.2 diesel. The jet penetration of No.2 diesel is slightly longer than that of the surrogate fuel. Moreover, the spray cone angle of the surrogate fuel is wider than that of No.2 diesel. In summary, the fuels of different thermophysical characteristics may develop and diffuse differently resulting in different characteristics of injection and atomization.