Ecological compensation is an applicable solution to support sustainable development of mega-regions, such as the Yangtze River Economic Belt (YREB), where conflicts often occur between environmental protection and economic growth. This study investigates the ecological footprints and carrying capacities of main cities in the Triangle of Central China based on a three-dimensional ecological model and the Gini coefficient. They are then used to generate ecological compensation schemes among sub-cities. The results have shown that ① the ecological footprints continued to increase from 2000 to 2015, with an annual growth rate of 7.52% (from 65.52 hm²/cap to 139.38 hm²/cap). The Wuhan Metropolitan Area and Xiang-Jing-Yi City Group occupied the most of regional ecological footprints growth. ② The ecological carrying capacity was decreased from 11.25 hm²/cap to 10.73 hm²/cap, and cultivated and forested lands were the major contributors from the perspective of land-use types. ③ The Gini coefficients of ecological footprints ranged from 0.425 to 0.488, and such a spatial distribution indicated an imbalanced and agglomerated tendency associated with city development. ④ Both of the payment area and the compensation amounts have increased during the past fifteen years, with the priority being Poyang Lake City Group > Great Chang-Zhu-Tang City Group > Wuhan Metropolitan Area and Xiang-Jing-Yi City Group. The outputs of this study are expected to provide decision-making suggestions for sustainable development of YREB, and offer valuable implications to other mega-regions as well.