Based on the construction needs and development status of new R&D institutions, the performance evaluation index system was constructed from the three dimensions of innovation input, operation level and innovation output. The index weight is determined by the combination of analytic hierarchy process and entropy weight method (AHP-EWM), and then the overall performance of three batches of new R&D institutions in Fujian Province from 2016 to 2018 was ranked by the TOPSIS method. The research shows that there are some problems in the construction of new R&D institutions in Fujian Province, such as large differences in development degree and weak industrial docking ability. Finally, the high-quality development countermeasures are proposed from the perspective of government management.