Herein, we have rationally designed and originally developed a high-performance deNOx catalyst based on hollow porous MnxCo3–xO4 nanocages with a spinel structure thermally derived from nanocube-like metal–organic frameworks (Mn3[Co(CN)6]2·nH2O), which are synthesized via a self-assemble method. The as-prepared catalysts have been characterized systematically to elucidate their morphological structure and surface properties. As compared with conventional MnxCo3–xO4 nanoparticles, MnxCo3–xO4 nanocages possess a much better catalytic activity at low-temperature regions, higher N2 selectivity, more extensive operating-temperature window, higher stability, and SO2 tolerance. The feature of hollow and porous structures provides a larger surface area and more active sites to adsorb and activate reaction gases, resulting in the high catalytic activity. Moreover, the uniform distribution and strong interaction of manganese and cobalt oxide species not only enhance the catalytic cycle but also inhibit the formation of manganese sulfate, resulting in high catalytic cycle stability and good SO2 tolerance. In light of the various characterization results, the excellent deNOx performance of MnxCo3–xO4 nanocages can be attributed to the hollow and porous structures, the uniform distribution of active sites, as well as the strong interaction of manganese and cobalt oxide species. The excellent catalytic performance suggests that MnxCo3–xO4 nanocages are promising candidates for low-temperature deNOx catalysts. More importantly, the present study indicates that the hollow porous architectures and well-dispersed active components can effectively enhance the performance of catalysts.