As China is undergoing economic transformation and facing increasing energy and environmental problems, it is essential to pay special attention to sustainable innovation governance. This research took industrial waste and total energy consumption into consideration and uses a super efficiency slack-based measure (SBM) model to empirically evaluate the regional innovation efficiency of Chinese provinces. The results showed that the efficiency of China’s regional sustainable innovation has not changed significantly over recent years. In addition, the results also showed large and varying degrees of innovation efficiency across different provinces. Eastern China, in comparison to central and western China, showed higher innovation efficiency. In addition, we found a slightly increasing trend in terms of innovation efficiency disparities between the three areas. On the basis of these findings, the reasons for the innovation efficiency gap between different regions were analyzed. The impacts of influential factors on sustainable innovation efficiency were further explored. We found that technology market maturity affected sustainable innovation efficiency positively, while government funding had a negative impact on sustainable innovation efficiency. Industrial structure and environmental regulations had no significant effect on sustainable innovation efficiency. Finally, some implications for improving governance performance in terms of sustainable innovation were provided.