In this paper we report a novel architecture of hierarchical 3D porous carbon microspheres (PCM) to encapsulate ZnO-CoO nanoparticles that serves as an advanced anode for high-performance lithium-ion battery (LIB). The PCM is fabricated by a facile aerosol spray pyrolysis method, and ZnO-CoO composite nanoparticles are infiltrated into the PCM by a simple one-pot hydrothermal procedure (i.e., ZnO-CoO@PCM). The developed hybrid material provides several advantages: (1) partial replacement of CoO with ZnO to offer a low-cost and eco-friendly candidate anode, (2) a continuous and large surface area (1236 m2 g−1) carbon network for improved electrical conductivity and uniform dispersion of ZnO-CoO nanoparticles, and (3) porous structure for good electrolyte diffusion and fast Li-ion transport and to buffer the large volume expansion of the metal oxides. As a result, this new ZnO-CoO@PCM nanocomposite demonstrates a higher reversible capacity (1250 mAh g−1 after 150 cycles at a current density of 100mAg−1), more excellent cycling stability, and better rate capability than a ZnO-CoO/PCM mixture and than a non-porous ZnO-CoO/carbon black mixture. The 3D porous nanocomposite architecture in this work could shed light on the design and synthesis of other metal oxides electrodes for energy storage.