There is a complex relationship of interdependence and mutual constraint in the water-energy-food system, and quantifying the interrelationships of the water-energy-food system is of great significance for the rational allocation and coordinated utilization of water, energy and food resources, as well as for promoting sustainable socio-economic development in the region. The models of energy and food production water footprint, competition index, decoupling theory and Theil index were applied to calculate and analyze the spatiotemporal variation characteristics of the water footprint of energy and food production in Sichuan Province from 2009 to 2019. It also explored the competition relationship between energy and food production for water and investigated the inherent connection between water footprint and gross domestic product (GDP). The research findings were as follows: both the water footprint of food production and the water footprint of energy production showed an increasing trend. The annual average blue water footprint of energy production was 5.45×109m3, accounting for 93.76% of the water footprint of energy production. The annual average blue water footprint of food production was 1.06×1010m3, accounting for 26.02% of the water footprint of food production, and the contribution of the green water footprint exceeded the sum of blue water footprint and grey water footprint, accounting for 53.06%. The competition index of water for energy and food production in Sichuan Province was on the rise, with an increase of 42.69%. Due to the consideration of both food and hydropower production in areas such as the Ecological Demonstration Zone in Northwest Sichuan and the Panxi Economic Zone, their competition index was significantly higher than that in other areas. The decoupling relationship between the water footprint and GDP of Sichuan Province was weakly decoupling and in a state of relatively coordinated development, indicating that economic development had a relatively good state of control over water consumption. The total difference in water footprint intensity showed an expanding trend, indicating that the unevenness of water use efficiency in Sichuan Province was gradually expanding, but it declined in the later period of the study, with a gradual convergence of development. The research result can provide suggestions for water resource allocation, energy development and food production in Sichuan Province, as well as for optimizing the economic development approach and the coordinated development of water use efficiency.