The innovation process cannot be completed independently. Research on the national innovation system (NIS) has attracted considerable attention. Such research reveals that it is critically important to understand that the operation of the NIS is both multi-stage and multi-dimensional, and ultimately shows its results in terms of national economic performance. From the multi-stage efficiency perspective, we built a three-stage network data envelopment analysis model to assess the R&D efficiency of knowledge creation fostered by the NIS, the diffusion efficiency of knowledge spillover and the economic efficiency of the economic achievements resulting from knowledge utilization. The study subjects consisted of 41 countries, including China, Brazil and OECD member countries. Finally, the efficiency results of NISs involve both cluster analysis and multidimensional scaling to make efficiency analysis concrete and vivid, as well as to serve as benchmark targets for inefficient NISs.