This paper constructs a comprehensive evaluation system of innovation quality from the process of innovation input-output, and calculates the comprehensive evaluation value of innovation quality in various regions of China by using the entropy method. This paper makes a dynamic comprehensive analysis of the innovation quality of the eastern, central, and western regions of China from 2008 to 2017. The results show that although China’s economy has been growing and innovation has increasingly become the focus of attention of the government and enterprises, the overall quality of innovation is not high, and there are obvious temporal and spatial differences. The innovation quality of the central and western regions is significantly lower than that of the eastern regions, and the differences show an expanding trend. And in recent years, the overall level of innovation quality in China has shown a downward trend.