The thermal transport properties of nanowires (NWs) can be significantly influenced by the implementation of a core-shell structure, which introduces interface scattering and phonon localization effects, opening avenues for novel applications. In this paper, we use the method of non-equilibrium molecular dynamics to simulate the effects of system temperature, cross-sectional width, and nanopillar interface on the thermal transport of GaN/Si3N4core-shell NWs. The thermal transport process of phonons in core-shell NWs is studied by calculating the vibrational density of states, phonon participation rate, and dispersion curve. The results show that the core-shell NWs characterized by smooth interfaces exhibit a 17.4% decrease in thermal conductivity (TC) at room temperature when contrasted with pristine GaN NWs. Furthermore, the TC of GaN/Si3N4core-shell NWs can be further reduced by adding nanopillars at the interface. Due to resonance effect, thus effectively regulating the thermal transport. The presence of nanopillars increases phonon-surface scattering intensity at low-frequency and modifies phonon dispersion to decrease the group velocity. In addition, the hybridization of phonon modes between those of the nanopillars and the Si3N4shell gives rise to numerous dispersionless resonance phonon modes that span the entire phonon spectrum. This research delves into the effects of nanopillars and interfaces on thermal transport, providing important guidance for understanding confinement effects and establishing a robust theoretical basis for the regulation of thermal transport.