Thermoplastic polyimides have garnered significant interest in the electronic and electrical industries owing to their performance characteristics. However, their relatively low thermal conductivity coefficients pose a challenge. To address this issue, this study focused on the properties of nanocomposites comprising two thermoplastic semicrystalline polyimides R-BAPB and BPDA-P3, one amorphous polyimide ULTEMTM, and hexagonal nanoparticles. Polyimide R-BAPB was synthesized based on 1,3-bis-(3′,4-dicarboxyphenoxy)benzene (dianhydride R) and 4,4′-bis-(4′-aminophenoxy)biphenyl (BAPB diamine); polyimide BPDA-P3 was synthesized based on 3,3′,4,4′-biphenyltetracarboxylic dianhydride (BPDA) and diamine 1,4-bis[4-(4-aminophenoxy)phenoxy]benzene (P3); and amorphous polyimide ULTEMTM was commercially produced by Sabic Innovative Plastics. Using microsecond-scale all-atom molecular dynamics simulations, the effects of incorporating hexagonal nanoparticles with enhanced thermal conductivity, such as graphene, graphene oxide, and boron nitride, on the structural and thermophysical characteristics of these materials were examined. The formation of stacked aggregates was found for graphene and hexagonal boron nitride nanoparticles. It was observed that graphene oxide nanoparticles exhibited a dispersion in polyimide binders that was higher than those in graphene and hexagonal boron nitride nanoparticles, leading to reduced translational mobility of polymer chains. Consequently, the decrease in polyimide chain mobility correlated with an increase in the glass transition temperature of the nanocomposites. Aggregates of nanoparticles formed a pathway for phonon transport, resulting in improved thermal conductivity in polyimide nanocomposites. An increase in the thermal conductivity coefficient of polyimide nanocomposites was observed when the concentration of graphene, graphene oxide, and hexagonal boron nitride nanofillers increased. The enhancement in thermal conductivity was found to be strongest when graphene nanoparticles were added.