One of the most important physical factors related to the thermal conductivity of composites filled with graphene nanoplatelets (GNPs) is the dimensions of the GNPs, that is, their lateral size and thickness. In this study, we reveal the relationship between the thermal conductivity of polymer composites and the realistic size of GNP fillers within the polymer composites (measured using three-dimensional (3D) non-destructive micro X-ray CT analysis) while minimizing the effects of the physical parameters other than size. A larger lateral size and thickness of the GNPs increased the likelihood of the matrix-bonded interface being reduced, resulting in an effective improvement in the thermal conductivity and in the heat dissipation ability of the composites. The thermal conductivity was improved by up to 121% according to the filler size; the highest bulk and in-plane thermal conductivity values of the composites filled with 20 wt% GNPs were 1.8 and 7.3 W/m·K, respectively. The bulk and in-plane thermal conductivity values increased by 650 and 2,942%, respectively, when compared to the thermal conductivity values of the polymer matrix employed (0.24 W/m·K).