Abstract: The long-term stability of the Yellow River basin depends on its systematic governance and the coordinated regulation of runoff and sediment. Factors maintaining the balance of runoff and sediment in the Yellow River include climate, ecology, topography, and significant human activities. Clarifying the boundaries of the subsystems that regulate the overall behavior of runoff and sediment, studying regulation indicators, and maintaining runoff balance are crucial for understanding the function of the river system. This study constructed a basin-channel-estuary coordinated regulation indicator threshold system to maintain the runoff and sediment balance of the Yellow River from a basin-wide perspective. The results showed a three-level threshold system for runoff and sediment regulation based on maintaining the balance throughout the basin. This system includes one primary indicator, eight secondary indicators, and twenty tertiary indicators. In the erosion prevention and control indicator threshold system at the basin level, the threshold value of secondary rainfall that can cause sediment production under 60% coverage of forest, grass, and terrace is 57 mm. The effective coverage rate of forest and grass, along with the threshold value of the terrace ratio that can control sediment production, is 60% and 40%, respectively. The sediment interception and erosion reduction threshold value for check dams is 40% to 50% of the third-level channel control rate. In the runoff and sediment regulation indicator threshold system at the channel level, the recent threshold value of bankfull discharge in the Ningxia-Inner Mongolia reach of Yellow River is about 2 000 m³/s, and the long-term threshold value after the completion of the Heishanxia Reservoir is approximately 2 500 m³/s. The recent elevation control threshold of Tongguan is around 328 m and may decrease to approximately 326 m due to erosion after the completion of the Guxian Reservoir. The threshold value of bankfull discharge in the lower reaches of the river channel is about 4 000 m³/s. Considering the dynamic balance of siltation and erosion in the Yellow River Delta, the threshold value of stable sediment discharge in the estuary is around 260 million t/a.