Ten Kongdui region in the Inner Mongolia section of the Yellow River Basin is facing the shortage of water resources caused by the overexploitation of groundwater and the predicament of “food and energy competing for water”. In view of this problem, the multi-dimensional water resources carrying capacity evaluation framework of “quantity-quality-domain-flow” was constructed, and the evaluation indicators were weighted subjectively and objectively using analytic hierarchy process and entropy weight method. Then the TOPSIS model was used to carry out the multi-dimensional comprehensive analysis of the regional water resources carrying capacity. The results show that the comprehensive carrying capacity of water resources in the study area showed an upward trend from 2000 to 2020, but the overall carrying capacity was in a critical carrying state; water resources dimension carrying capacity is ranked as follows: quantity>flow> quality>domain, and water resources subsystem carrying capacity is ranked as follows: water use pattern>carrier>carrying object. Overall, the rigid constraints of the “three red lines” of the country’s most stringent water resources management system and the full implementation of the river and lake chief system have forced the regional water resources to increase their carrying capacity in the “quality” and “flow” dimensions. However, continued high-intensity water resources development and utilization have significantly reduced the carrying capacity of the “volume” and “domain” dimensions. In the future, it is necessary to further optimize the water use pattern of agriculture and industry, focus on solving the problem of “food and energy competing for water”, and increase the diversion of the existing river and lake water resources to achieve sustainable social and economic development and water resources load balance.