Low-carbon energy technology (LC) innovation contributes to both environmental protection and economic development. Using the panel data of 30 provinces/autonomous regions/municipalities in China from 1998 to 2017, this paper constructs a two-layer logarithmic mean Divisia index (LMDI) model to uncover the factors influencing the variation of the innovation of LC in China’s industrial sectors, including the alternative energy production technology (AEPT) and the energy conversation technology (ECT). The results show that China’s industrial LC patent applications rapidly increased after 2005 and AEPT patent applications outweighed ECT patent applications all the time with a gradually narrowing gap. Low-carbon degree played the dominant role in promoting the increase in China’s industrial LC patent applications, followed by the economic scale, R&D (research and development) efficiency, and R&D share. Economic structure contributed to the increases in LC patent applications in the central and the western regions, while led to the decreases in the eastern region, the north-eastern region, and Chinese mainland . Low-carbon degree and economic scale were two main contributors to the growths of both industrial AEPT patent applications and ECT patent applications in Chinese mainland and the four regions. Several policy recommendations are made to further promote industrial innovation in China.