This work is aimed towards studying and analyzing the heat transfer performance in a novel 3D graphene-carbon nanotube (CNT) pillared structure. Although both graphene and CNT are known to have high thermal conductivity in in-plane and along the axis, respectively, they have low thermal conductivities in the other directions. Hence, the 3D graphene-CNT structure will have high thermal conductivities in both in-plane and out-of-plane directions due to the pillared architecture. It can be applied to small-scale electronic devices for high efficient heat dissipation and/or exchange. The pillared structure consists of few-layer graphene (FLG) and bundles of CNTs. CNT bundles connect between two sheets of FLG. The heat transfer performance of the structure was investigated through a continuum model by COMSOL Multiphysics. Parameter studies were conducted to determine the optimum graphene-CNT configuration, including number of CNTs in each bundle, number of bundles in the structure, distance between bundles (a.k.a. inter-pillar distance “IPD”), length of CNT, and the arrangement of CNT bundles. Results of the simulations concluded that (1) the reduced IPD could prevent the in-plane heat spreading, (2) the increased number of CNTs could enhance the axial-direction thermal transport, and (3) the arrangement of CNT bundles between FLG sheets (e.g. shifting one row of CNT bundles) has minor impacts on the overall heat transfer performance of the structure.