Three-dimensional thermal interface materials made of graphene oxide (GO) and copper nanoparticles (Cu NPs) were applied for enhancing light-emitting diode heat dissipation. The effect of the stacking order of GO and Cu NPs on thermal resistance was explored by creating two types of samples: spray-coated with a mixed GO-Cu NPs and layer-by-layer stacked with GO/Cu NPs/GO. A reduction of thermal resistance for mixed GO-Cu NPs and layer-by-layer stacked structure by 37% and 33%, respectively, compared to that of Al heat sink. The lower thermal resistance of the mixed GO-Cu NPs sample is attributed to the fact that distributed Cu NPs at the step edge of GO sheets enhances the out-of-plane heat transfer at wrinkles/folds of GO interlayers. Therefore, a mixed GO-Cu NPs is considered as a promising composite for effective thermal management of high-performance optoelectronic devices.