Based on the analysis for economy and science of multinational R&D invested region, 13 index indicators are selected in this paper to establish the multinational R&D investment Environment-Friendly Evaluation System of China. The empirical research is carried out on 31 provinces of China with principle componential analysis and clustering analysis. Firstly, the main component is extracted from the 13 indexes with principle component analysis, and the comprehensive rank is concluded based on principle component function; Secondly, as far as comprehensive rank is concerned, clustering analysis is used to rank the investment environment to four clusters (A, B, C, D). Finally, the key factors can be obtained which affect the R&D investment environment-friendly through the result of empirical research, and play an important role in choosing and improving the R&D investment regions.