Abstract: Taking 30 provinces in the four regions of East, middle, West and Northeast China as the research objects, an innovation performance evaluation system is constructed in two stages, scientific and technological achievement output and scientific and technological achievement transformation. The situation of industry-university-research collaborative innovation from 2015 to 2019 is systematically analyzed by two-stage Data Envelopment Analysis(DEA) and Malmquist index methods. The results are as follows: (1) In the stage of achievement output, 63% of the provinces have achieved effective DEA, the overall performance of the central region is the best, and the eastern region is relatively poor. In the stage of achievement transformation, only 50% of the provinces have achieved DEA effectiveness, and contrary to the first stage, the overall performance of the eastern region is well, and the central region is at the bottom of the list. (2) The growth rate of innovation performance in the achievement transformation stage is higher than that in the achievement output stage. (3) The effectiveness of comprehensive efficiency in the Western region is least stable. The Northeast region has achieved a zero breakthrough in the effectiveness of comprehensive efficiency, and the effectiveness of comprehensive efficiency in the central region is improving in an orderly manner. The Eastern region should optimize the allocation of scientific and technological factor resources, improve the output efficiency of scientific and technological achievements. While Northeast China should strengthen industry-university-research cooperation, improve the transformation efficiency of scientific and technological achievements, as well as promote cross regional cooperation and innovation to ensure the coordinated improvement of innovation performance.