This work firstly aims to analyse the balance between tangibles and intangibles as well as among human capital, structural capital and relational capital of evaluation indicators for the research institutes in science and technology sector conducted in 2006, by adopting intellectual capital model. The research question of this work comes from that while the R&D activity can produce both tangibles and intangibles, there have no been methodologies to relevantly measure and rationally judge these, in particular, intangible performance. The result shows that the institute evaluation system in 2006 had given more weight on tangibles and structural capital than intangibles and other intellectual capitals such as human capital and relational capital, in comparison to the past evaluation system, even though, in principle, the current evaluation system has to deal with the intangible research performances as well as tangible ones in economic, social and cultural perspective. Finally, based on these analysis, I will try to suggest some policy directions for overcoming the deficits of indicators in institute evaluation system.