To identify the coordinated development status and limiting factors of water and sediment-ecology-economy in various intervals of the Yellow River Basin under influence of reservoir group operation, a comprehensive evaluation index system considering the impact of reservoir regulation and storage was constructed. An improved TOPSIS joint grey relational analysis model was established, and corresponding coupled coordination degree models and obstacle degree models were proposed. The results show that from 2000 to 2022, the development index of water and sediment, ecology, and economic subsystems in the upper, middle, and lower reach intervals of the Yellow River Basin showed an increasing trend and generally a lagging type of water and sediment subsystem, and their development index was significantly linearly correlated with the inflow. The overall coordinated development degree of each interval has improved, and the lower reach interval has remained stable at a good coordination level. The upper and middle reach intervals have fallen back to a medium coordination level since 2021. The coordinated development of the basin is mainly constrained by the water and sediment subsystem, which is more prominent in drought years. The upper reach interval is mainly constrained by the total amount of water resources and development utilization rate, while the middle and lower reach intervals are also constrained by factors such as reservoir sediment discharge ratio and river channel erosion and deposition. In the ecology and economy subsystems, impermeable area, fertilizer application intensity, habitat index, urban-rural disposable income ratio, and per capita domestic water consumption are the main limiting factors.