In this paper, hollow nanospheres (HNSs) of metal oxides (NiO, CuO, and NiO/CuO) coated with a porous carbon shell (HNSs@C) with good structural stability were successfully prepared on the basis of the nanoscale Kirkendall effect. The formation process was based on a template-free method, and the as-prepared HNSs@C are very clean compared with products of the template process. In addition, the results of N2 adsorption–desorption noted that both the metal oxide HNSs and the coated carbon were mesoporous structures. Therefore, small molecules can access the inner space of the whole HNSs@C, which was expected to increase the active site area and to show better performances in applied fields, such as catalysts and sensors. As an example of the functional properties, the obtained HNSs@C were investigated as the catalyst for the hydrogenation of 4-nitrophenol (4-NP) and manifested highly catalytic activity and excellent stability. This work has opened up a novel route for the development of metal oxide HNSs nanocatalysts. This straightforward method is of significance for development of clean metal oxide HNSs with high stability and multiplied applications.