In order to explore the evaluation program of non-enterprise scientific and technological activities, and correctly evaluate the scientific and technological innovation capability of various cities in Shandong, the innovation capability of non-enterprise scientific research activity units in Shandong Province was evaluated, and the evaluation index system was constructed including 10 indexes at two levels of scientific and technological innovation resources and scientific research output. Factor analysis of scientific and technological innovation resources and scientific research output and overall data of scientific research non-enterprise scientific and technological activity units was performed, and the comprehensive score of the innovation level of each city is obtained. According to the score of evaluation , the countermeasures and suggestions are put forward to strengthen the innovation ability of the scientific research and technological activity units in Shandong Province.