With the socio-economic development in China, the central government pays more and more attention to innovations. Universities, research institutes, and industries (URI) are the main bodies of innovation. Therefore, in order to perform sustainable development of innovation, it is essential for Chinese policy makers to better understand the relationship among URI innovations. In this paper, indicators for evaluating URI innovations are collected, which are classified into three subsystems. Utilizing regional data from 2009–2015 in China, the entropy method is subsequently used to examine the contribution of indicators to the relative innovation subsystems. Then, a coupling coordination degree model is developed based on the physical concept “coupling” to investigate the relationship of URI innovation subsystems in China. The results reveal that in the period of study: (1) research and development (R&D) input and output indicators are both important to the regional innovation levels of URI, namely, they are critical for improving the coupling coordination degree among the three innovation subsystems; (2) There is an increasing trend of the coupling coordination of URI innovation system in China; however, the gap between regions/provinces becomes larger due to different innovative resource endowments and socio-economic development conditions. The results shown in this paper can provide important implications for policy makers to obtain the sustainable development of URI innovation subsystems in China.