Low-carbon transformation has become the main path towards achieving sustainable development of natural resources industries. However, little is known about how low-carbon transformation can be realized while maintaining economic growth in natural resources industry under COP26 targets. To address this issue, we investigated the regional carbon emission efficiency of natural resources industry, and explored the determinants of achieving higher carbon emission efficiency. Specifically, this research adopts a Super-SBM model with undesirable outputs approach to estimate the regional carbon emission efficiency of natural resources industry in each province of China over the period of 2008-2019. Further, we identify and examine the determinants of carbon emissions efficiency by constructing a panel fixed-effect model. We have the following findings: (1) Carbon emissions efficiency exhibits an increasing trend in different regions and shows a regional clustering effect, e.g., the carbon emissions efficiency in the eastern regions is generally higher than in other regions. (2) When green innovation activity level, environmental regulations intensity, education level of human capital, and openness of the focal region are higher, the value of carbon emissions efficiency of its natural resources industries is larger. Economic development level has a significantly negative effect on the regional carbon emissions efficiency. (3) Green innovation activity level has the highest importance among all five determinants. Policy recommendations for policymakers concerning improving green innovation activity level, human capital, environmental regulations intensity, and openness were also discussed.