Migration and distribution of thermal conduct fillers in polymer blend are key factors in the preparation of enhanced thermal conductivity composite. In this study, polystyrene(PS)/polyamides 6(PA6)/graphene nanoplatelets(GNPs) composites with enhanced thermal conductivity were prepared under elongational flow, and the migration and distribution of GNPs were investigated by molecular dynamics simulation and experiments. The results showed that when GNPs immigrate from PA6 phase to PS phase, the elongational flow caused the orientation of the PS phase and GNPs, reducing the migration rate of GNPs from the PA6 phase to the PS phase. At the same time, the stretching viscosity of the PS phase increases, which prevents GNPs entering the PS phase. As a result, GNPs remain within the PA6 phase near the interface of the two phases. The effective distribution density of GNPs increased, making it easier for them to interconnect and form thermal conduction paths, thereby improving the thermal conductivity of the composites. Particularly, the composite prepared under the elongational flow with the 50/50 vol ratio of PS/PA6, the in-plane thermal conductivity of PS/PA6/GNPs composites reached a maximum of 1.64 W/(m·K).