This paper compares R&D efficiency across countries based on various output-oriented R&D efficiency indexes that are developed by data envelopment analysis (DEA) approach. Empirical results show that countries have similar R&D efficiency in terms of patents and royalties, while their performance on journal publications is quite different. We then apply the Tobit regression to investigate how the innovation environment, especially in the national innovation system, affects these output-oriented R&D efficiency indexes. R&D intensity, intellectual property rights protection, knowledge stock, and human capital accumulation all have positive effects on efficiency indexes. Meanwhile, private sector R&D funded by either foreign sources or funded and performed by private businesses plays an important role in improving scores on the output-oriented R&D efficiency index for patents and for royalties and licensing fees. The R&D intensity performed by higher education institutions has a positive effect on scores on the journal-oriented R&D efficiency index.