Accelerating the transformation of the rural energy structure is an indispensable part of energy transformation in developing countries. In this novel study, the transformation effect of China’s rural energy structure from 2001 to 2020 was evaluated. Further, this paper also identified the decoupling state between the rural energy structure transition and carbon emissions, and decomposed the spatial–temporal effects of rural carbon decoupling through efficiency measures. According to the survey, the dual substitution index of the rural energy structure in China increased from 0.466 to 1.828, and showed a decreasing trend in spatial distribution from the east to the central and western regions. Economic development and climate characteristics have become important influencing factors for the dual substitution of the rural energy structure. The decoupling relationship between the dual substitution of the rural energy structure and carbon emissions was mainly characterized in the strong decoupling, expansion negative decoupling, and strong negative decoupling states. Regional imbalances have deepened as the efficiency of rural energy carbon decoupling has gradually increased. The annual average efficiency of rural energy carbon decoupling in a dynamic perspective has increased by 10.579%, and the dual substitution of the energy structure has a significant driving effect on rural carbon reduction.