Excellent mechanical properties are the lifeline for the application of solid propellants. Understanding the strengthening mechanism of bonding agent is of great significance for design and application of high-performance bonding agents. In this study, the strengthening mechanism of neutral polymer bonding agent (NPBA) for the NEPE propellant and dynamic mechanical response were explored through MD simulation. Significant difference in bonding role for RDX and HMX surface is first revealed with a more effective improvement in HMX surface. NPBA requires higher peak pulling force to achieve conformational transformation compared with binder throughout the peeling process. The chain orientation and movement undergo significant changes in nitroglycerin environment and an interface peeling model is proposed to reveal the potential mechanism. Finally, the effect of NPBA insertion on interfacial micro-peeling process indicates that no significant detachment of NPBA until the binder was severely deformed, resulting in a higher pulling force required.