In this article, Molecular dynamics (MD) simulation were applied to investigate the adsorption behavior and mechanism of neutral polymeric bonding agents (NPBA) in nitrate ester plasticized polyether (NEPE). The simulation results indicate that due to the strong van der Waals (vdW) force interaction, NPBA has the highest binding energy with RDX compared to PEG and nitrate plasticizer. Then, the influences of temperature on the compatibility of nitrate plasticizer and two polymers, NPBA and PEG, were studied. The results show that PEG can dissolve in nitrate plasticizer over a wide range of temperature, while the compatibility of NPBA and nitrate plasticizer decrease with the reducing of temperature. Moreover, the adsorption behavior of the NPBA on RDX surface in nitrate plasticizer was investigated. The results demonstrate that the NPBA chains can penetrate through nitrate plasticizer, adsorb on the RDX surface, and form a compact protection layer, which prevents the bonding interface from nitrate plasticizer damage. Our researches afford a microscopic insight into the mechanism of NPBA, and can be helpful to the NPBA molecular and NEPE formulation design.