Molecular dynamics (MD) simulation and experimental methods are used to explore the interaction between the propargyl-terminated polybutadiene (PTPB) binder and plasticizers bis(2,2-dinitropropyl) formal/acetal (BDNPF/A) and dioctyl sebacate (DOS). Flory-Huggins parameters, radial distribution functions, and binding energies between PTPB and plasticizers are calculated using MD simulations. The solubility parameters of PTPB and the plasticizers are calculated by both MD and group contribution method. The mesoscopic dynamics (MesoDyn) is used to simulate the meso-morphology of PTPB and plasticizer blends by converting the results of MD simulation into MesoDyn simulation parameters. The results of simulations and calculations show that PTPB has better compatibility with DOS than with BDNPF/A, and DOS is more suitable as a plasticizer for PTPB. The results of dynamic rheological experiments show that BDNPF/A has little effect on the dynamic viscosity of PTPB, and DOS can significantly reduce the dynamic viscosity of PTPB and has better plasticizing effect on PTPB. Differential scanning calorimetry and dynamic mechanical analysis tests indicate that the DOS and PTPB blend has only one glass transition temperature, while the PTPB and BDNPF/A blend has two glass transition temperatures. Both simulations and experimental results show that the PTPB binder have better compatibility with DOS than with BDNPF/A, and DOS has better plasticization effects on the PTPB binder.