Critical geographical mismatch between limited water availability and increasing demand brings tremendous challenges to ensuring sustainable food and energy security in China. Most previous studies measuring the spatial mismatching characteristics are based on one paired nexus as food-water or energy-water, yet few have characterized the spatial-temporal variations of FEW nexus inequality and further investigated the hidden drivers under a unified system boundary when involving all the three subsystems. From a nexus perspective, the quantitative analysis of the inequality pattern and evolving trend would provide the sound basis for appropriate allocation and coordinated management of water-energy-food resources. Therefore, this study systematically calculated the blue water footprint of food (rice, wheat, maize, beans and tubers) and main water-consumptive energy (raw coal, crude oil, natural gas, thermal power generation) production in 30 provinces of mainland China during 2000-2019, aiming to characterize the inequality against water availability at both the national and regional scales, by combing the Gini coefficient and unbalanced index. Additionally, the driving forces in view of resources endowment and production structure were also identified. The results showed that:(1) the Gini coefficient of food-water nexus was always kept around 0.35 over the last two decades, while that for energy-water nexus was higher with a U-shaped symmetrical change (G=0.43-0.62), manifesting a greater spatial inequality between energy production and water availability at the national scale. In terms of different resource types, rice, as the water-intensive crop, performed best, compared with wheat, corn, raw coal and thermal power. (2) the food-water nexus and energy-water nexus both presented type-Ⅰ inequality in northern regions, which has extended westward from the northern and eastern coastal regions during the concern period, compared with type-Ⅱ in southern regions. Typically, Heilongjiang converted from significant type-Ⅰ inequality to low type-Ⅱ. (3) changes in water availability and rice production transfer to the north were the main causes of changes in food-water nexus inequality. While it was mainly due to the westward development of thermal power industries with regard to changes in energy-water nexus inequality, except for the greater impact by crude oil reduction in Heilongjiang province. (4) the spatial relationship of food-water resources was mainly affected by crop properties, economic benefits and agricultural policies, while it turned to fossil fuel reserves, economic disparities and environmental policies in terms of energy-water resources. Results obtained in this study could shed light on water-energy-food resources management, by strengthening general plan, optimizing spatial distribution, accelerating industrial restructuring, improving water use efficiency, and enhancing regional cooperation.