The two-dimensional (2D) graphene sheets show superior electrical, thermal and mechanical properties. The three-dimensional (3D) graphene assemblies have also recently garnered great attention because of their high surface area, free-standing configuration and facile fabrication of graphene composites with nanomaterials in practical applications. Herein, we demonstrate the synthesis of a variety of 3D graphene assemblies including spheres, twiddles and hemispheres using micro-droplet reactors. Such 3D reduced graphene oxide (rGO) structures can be manipulated by controlling the aggregation pattern of the GO sheet inside the micro-droplets. The aggregation pattern depends on the diffusion rate of the aqueous solution in the droplet. The pattern was simply tuned by the amount of oil phase in the droplet during evaporation. In addition, micro-porous structures were manufactured by incorporating silica beads in the rGO microparticles, followed by a wet etching process. The local plasmonic properties of the 3D porous hemispherical rGO were investigated by electron energy-loss spectroscopy mapping.