The household energy mix, especially the sustainable use of affordable clean energy, is an important part of society and is closely related to many sustainable development goals. The proportion of the population mainly using solid fuels or clean energy is widely considered, but multiple energy carriers (energy stacking) used in the real world result in considerable biases in the results in which only primary energy was counted. From a nationwide survey on the household energy mix in rural China, the present study revealed that in 2012, nationally, the average numbers of cooking energy carriers and heating energy sources were 3.4 and 2.5 per household, increasing from 2.0 and 2.2 per household in 1992, respectively. Within the country, the spatial difference in the household number of household energy carriers was negatively associated with the family income level and explained by the affordability and faster clean energy transition. In 2012, the proportion of people extensively using gas or electricity for cooking was 32% and 27% for heating, respectively. The proportion increased substantially over time from 1992 to 2012, indicating an obvious switch to cleaner household energy sources. The absolute number of rural people using clean-household energy was increasing, despite the reduced rural population under urbanization. The proportion of people using clean-household energy for more than half of the time per year for cooking and heating was 56% and 32% , respectively. The results were higher than the proportion of people extensively using clean-household energy, and the difference was larger with more types of different energy sources used in households, particularly for cooking. It is imperative to consider multiple energy uses in household surveys and to call for more field work regarding household energy mix transitions as an integral part of sustainable development research.