As the continuous improvement of the quality of innovation becomes increasingly significant for balanced regional development in China, it is critical to provide insights into the sustainability of regional innovation in China from the viewpoint of value. This study estimates regional innovation values based on an improved regional innovation value model incorporating patent values and a regional innovation indicator system. Data for invention patents as well as regional innovation indicators in 282 cities from 1987 to 2019 in China are utilized for estimation. Based on the estimated parameters and Monte Carlo simulation, city-level innovation values are calculated as benchmarks, along with provincial and regional innovation values, to analyze the patterns of the spatial distribution and agglomeration of regional innovation value. The findings are as follows. (1) The regional innovation value model provides an effective way to measure regional innovation in terms of value. (2) The regional innovation values are unevenly distributed; cities with higher innovation values are clustered in Eastern China, while most other cities have much lower innovation values. (3) The innovation values in Eastern China are notably higher, and the differences in innovation values between Eastern China and other regions are large and show a trend of first widening and then narrowing during the sample period. (4) The sustainability of regional innovation is not widely achieved, since highly concentrated innovation value is found in only a few regions in the eastern coastal areas. These findings suggest that promoting China’s innovation capacity and the sustainable development of technological innovation requires continually implementing innovation-driven development strategies, cultivating high-value innovation, optimizing industrial transfer, improving the layout of the national research infrastructure, giving full play to spatial spillover effects, and promoting interregional innovation information exchange in order to achieve the balanced and sustainable development of regional innovation.