Molecular dynamics simulation was applied to investigate the sensitivities of perfect and defective RDX (cyclotrimethylene trinitramine) crystals, as well as their PBXs (polymer-bonded explosives) with the polymeric binder F2311, in the NPT (constant number of particles, constant pressure, constant temperature) ensemble using the COMPASS force field. Five kinds of defects—two dislocations, one vacancy, and two types of doping—were considered separately. The bond length distribution and the maximum (L max) and average (L ave) bond lengths of the N–NO2 trigger bonds in RDX were obtained and their relationships to the sensitivities of RDX and PBXs are discussed. L max was found to be an important structural parameter for judging the relative sensitivity, and defects were observed to have little effect on the sensitivities of PBXs, due to the strong desensitizing effect of the polymer F2311.