Ecological watersheds (eco-watersheds) are of great significance for boosting the construction of ecological civilization and realizing the ecological protection and high-quality development of watersheds. In order to establish a scientific eco-watershed evaluation index system, this paper refers to the river health evaluation index system, the water resources coupling evaluation index system, and the happy river evaluation index system, and reviews the development process of the ecological watershed evaluation index system. According to the eco-watershed theoretical system, combined with the relevant contents of policies and regulations, thousands of evaluation indicators that have been collected are screened using the theoretical analysis method and the frequency analysis method. Finally, a comprehensive evaluation index system of Weihe River eco-watersheds was constructed, including three first-level indicators: watershed water resources, socio-economic, and ecological. These were further subdivided into eight second-level indicators, namely water security, water resources, water economy, water management, water culture, water environment, water ecology, and water landscape. These second-level indicators were then further broken down into 60 third-level indicators. On the basis of determining the evaluation standards of Weihe River eco-watersheds, the evaluation weights were determined using the gray correlation method and the AHP-entropy comprehensive weight method (comprehensive weight), resulting in the establishment of an evaluation model and a coupling model for the eco-watersheds of the Weihe River. The results of the Weihe River eco-watershed evaluation model and the coupled coordination degree evaluation model show that, from 2019 to 2021, both the gray correlation analysis weights and comprehensive weight evaluation show a yearly increasing trend; the evaluation results are in the eligible status and below; and the evaluation grade is in the fourth-level eco-watersheds and below. Based on the evaluation results of each dimension, when comparing the gray correlation analysis weights with the evaluation of the comprehensive weights, the latter align more closely with the actual Weihe River Watershed. When comparing the evaluation results of the Henan Weihe River Watershed with those of the Handan Weihe River Watershed, the latter’s results, influenced by the scheduling of the Yuecheng Reservoir, are relatively better. Furthermore, in the evaluation of coupling coordination, the water resources subsystem is less coupled to other subsystems due to the 2021 flood. Therefore, in order to effectively improve the level of eco-watersheds, scientific and reasonable water resources scheduling programs should be developed.