A decoupling physical-chemical surrogate (DPCS) model was established for simulation of the spray and combustion characteristics of multi-component biodiesel fuels. In the DPCS model, the physical and chemical properties of biodiesel fuels are described separately. For the case study of soybean methyl ester (SME), the physical properties are represented based on the five primary components, i.e., methyl palmitate, methyl stearate, methyl oleate, methyl linoleate, and methyl linoleate. Meanwhile, the chemical kinetics of SME are described by a skeletal reaction mechanism composed of methyl decanoate, methyl 5-decenoate, and n-decane. Furthermore, an improved quasi-dimensional multi-component vaporization model was applied to predict the fuel vaporization process. To validate the DPCS model, the predictions from the present model and the previous models are compared with the experimental data, including the liquid penetration in a constant-volume bomb and the combustion and emission characteristics in a premixed charge compression ignition (PCCI) engine. The results indicate that the predictions of the DPCS model agree better with the measurements than the previous models considering only the single-component physical and/or single-component chemical properties of SME on the spray, ignition, and combustion behaviors. It is found that the ignition delay and heat release rate of PCCI combustion are dominated by the evaporation rate of SME and the fuel-reactivity stratification within the cylinder. By considering the multi-component properties of SME, the combustion and emission characteristics can be satisfactorily reproduced by the DPCS model. Meanwhile, the computational time can be well controlled due to the simplification of the physical and chemical surrogate sub-models.