A high-performance anode material, NiCo2O4/3DHPC composite, for lithium-ion batteries was developed through direct nanoparticles nucleation on a three-dimensional hierarchical porous carbon (3DHPC) matrix and cation substitution of spinel Co3O4 nanoparticles. It was synthesized via a supercritical carbon dioxide (scCO2) expanded ethanol solution-assisted deposition method combined with a subsequent heat-treatment process. The NiCo2O4 nanoparticles were uniformly embedded into the porous carbon matrix and efficiently avoided free-growth in solution or aggregation in the pores even at a high content of 55.0 wt %. In particular, the 3DHPC was directly used without pretreatment or surfactant assistance. As an anode material for lithium-ion batteries, the NiCo2O4/3DHPC composite showed high reversible capacity and improved rate capability that outperformed those composites formed with single metal oxides (NiO/3DHPC, Co3O4/3DHPC), their physical mixture, and the composite prepared in pure ethanol (NiCo2O4/3DHPC-E). The superior performance is mainly contributed to the unique advantages of the scCO2-expanded ethanol medium, and the combination of high utilization efficiency and improved electrical conductivity of NiCo2O4 as well as the electronic and ionic transport advantages of 3DHPC.