In order to explore more effective approach in molecular design of neutral polymeric bonding agent(NPBA) than semi-empirical and semi-quantitative method, MesoDyn module of Materials Studio was used to simulate mesoscopic phase segregation of three NPBAs in energetic plasticizer/prepolymer mixture, as described in U.S. Patent No.4915755. It is shown that the order parameter of NPBA in the mixture at 303 K (30 ℃) is higher than that of the NPBA at 333 K (60 ℃), which means that phase segregation at low temperature is stronger and agrees well with the goal of NPBA tailoring. On the other hand, increasing molecular mass of NPBA and percent of NPBA in the mixture and decreasing processing temperature can increase phase segregation. These results can be explained by related theory of polymer solution and indicate the mesoscopic simulation method can be used for verifying of NPBA molecular design in a straightforward way.