Toughened paraffin wax applied in polymer bonded explosives(PBXs) is mainly to improve its mechanical properties. In this paper, based on the study of toughened paraffin, four kinds of formulations of toughened paraffin and plasticizers were designed. The blending models of styrene-butadiene-styrene block copolymer(SBS) toughened paraffin Wax with dibutyl phthalate(DBP), dioctyl sebacate(DOS), nitroglycerin(NG) and acetyl tributyl citrate(ATBC) were established. The compatibility of the toughened Wax with plasticizers and the nature of the intermolecular interactions in the blend systems were simulated and studied by molecular dynamics method. Results show that the compatibility of SBS toughened Wax with plasticizers can be comprehensively evaluated by the four criteria of solubility parameter, miscibility simulation, binding energy and intermolecular radial distribution function. In which, the relative error between the simulated value and the experimental one of solubility parameter is within 3% and the miscibility simulation can quickly predict the compatibility between two substances. The binding energy of ATBC and SBS toughened Wax is the largest, which is 2.7 kJ·g^-1. The essence of the interaction between SBS toughened Wax and plasticizers is van der Waals force and electrostatic force, mainly to van der Waals. The compatibility sequence of the three plasticizers with SBS toughened Wax is ATBC> DOS> DBP, NG is incompatible with SBS toughened Wax.