在科技競爭的年代，科研組織的績效表現攸關一國的創新能力與競爭力。由於大量的政府預算投注於科研機構，也使得科研組織的績效評估，不論在支援決策、激勵人才、促進組織的學習與持續改善，或與外界的溝通與合作上，都是非常重要的議題。本文首先回顧科研組織績效評估相關理論與文獻的發展，經分析後提出一套結合效能與效率、平衡計分卡及智慧資本等多種概念的科研組織評估架構，並將此評估架構分為效能、效率與發展能量三個評估層次，再依此架構發展出一些適當的評量指標。本文發現，現行國科會的組織評估機制指標系統龐大，同時也缺乏資料分析方法，不利於決策者判讀資訊，因此發展出較為精簡的指標系統以及分析方向，應能有效提升決策者的資訊品質與決策效率。

Science and technology (S&T) research institutes are the center of the national innovation system (NIS). As such, it is very important to have an adequate measurement system in the NIS to appraise the performance of research institutes. This system should function to encourage researchers, to improve research institutes, to intensify the cooperation between institutes, and to help the formation of decision support system of S&T policies. This paper aims to develop a performance measurement system and indexes of S&T research institutes. Based on several theoretical structures of performance measurement, we construct a new measurement structure for S&T research institutes, which combines the concepts of effectiveness, efficiency, balanced scorecard (BSC) and intellectual capital. In this structure the appraisals are based on three different dimensions: effectiveness, efficiency and development capacity. While assembling measurement dimensions and indexes, this paper found that the indexes of current performance measurement system operated by
the National Science Council (NSC) of Taiwan are kind of complicated and
short of systematical data analysis, which may hinder the quality and efficiency of the decision-making of S&T policies. As such, this paper provides several simplified indexes and suggests some directions of measurement analysis in order to improve the functions of overall performance measurement system of S&T research institutes in Taiwan.