With the supply of water, energy and food facing severe challenges, there has been an increased recognition of the importance of studying the regional water–energy–food nexus. In this paper, Inner Mongolia, including 12 cities in China, was selected as a research case. A super-efficiency slack based measure (SBM) model that considered the undesirable outputs was adopted to calculate the regional total factor productivity (TFP) and the Malmquist–Luenberger index was used to investigate the change trend of the TFP from 2007 to 2016 based on understanding the water–energy–food nexus. Finally, influential factors of the TFP were explored by Tobit regression. The results show that the 12 Inner Mongolia cities are divided into higher, moderate and lower efficiency zones. The higher efficiency zone includes Ordos, Hohhot, Xing’an, and Tongliao, and the lower efficiency zone includes Chifeng, Xilin Gol, Baynnur, Wuhai and Alxa. There is a serious difference in TFP between Inner Mongolia cities. During the study period, the TFP of the water–energy–food nexus in Inner Mongolia cities shows a rising trend, which is mainly driven by the growth of technical progress change. However, the average ML values of the lower and moderate efficiency zones were inferior to the higher efficiency zone in six of the ten years, so the difference between Inner Mongolia cities is growing. According to the Tobit regression, the mechanization level and degree of opening up have positive effects on the TFP, while enterprise scale and the output of the third industry have negative effects on the TFP. Government support does not have any significant impact on the TFP. Finally, suggestions were put forward to improve the TFP of the water–energy–food nexus in Inner Mongolia cities.
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