Due to the rapid growth of the population and the development of economies in the Guanzhong district, central China, the river ecosystem is gradually deteriorating, which makes it important to assess the aquatic ecosystem health and take measures to restore the damaged ecosystem. An index of catchment ecosystem health has been developed to assist large-scale management of watersheds by providing an integrated measure of ecosystem health, including aquatic and terrestrial ecosystem. Most researches focus on aquatic ecosystem or terrestrial ecosystem, but little research integrates both of them to assess the catchment ecosystem health. In this paper, we combine these two aspects into catchment ecosystem health. Ecosystem indicators derived from field samples and modeling are identified to integrate into ecosystem health. These included indicators of ecological landscape pattern (based on normalized difference vegetation index (NDVI), vegetation cover, dominance index, Shannon's diversity index, Shannon's evenness index, and fragmentation index), hydrology regime (based on 33 hydrological parameters), physical form condition (based on substrate, habitat complexity, velocity/depth regimes, bank stability, channel alteration), water quality (based on electrical conductivity (Cond), dissolved oxygen (DO), NH3_N, total nitrogen (TN), total phosphorus (TP), chemical oxygen demand-permanganate (CODMn)), and biological quality (based on fish abundance). The index of ecosystem health is applied in the Guanzhong district, and the ecosystem health was fair. The ecosystem health in the upstream to Linjiacun (U-L) and Linjiacun to Weijiabao (L-W) reaches was in good situation, while that in Weijiabao to Xianyang (W-X), Xianyang-Weijiabao (X-W), and Weijiabao to Tongguan (W-T) reaches was in fair situation. There is a trend that the ecosystem health in the upstream was better than that in the downstream. The ecosystem health assessment is expected to play a key role in future water and watershed management of the Wei River basin, or even the Yellow River basin.