The Yellow River, often referred to as the mother river of China, plays a crucial role in the country's economic, social, and ecological development. It serves as a significant economic zone, an essential ecological barrier, and a key area in the fight against poverty. Within the Yellow River Basin, the Pisha stone area is highly eroded and is the primary source of the Yellow River's coarse sediment, posing a major threat to the river's security. However, it is also a key node in China's “Silk Road Economic Belt,” playing a crucial role in the country's “Belt and Road” strategy. Thus, the ecological management of the Pisha stone area has become the most prominent shortcoming in the comprehensive management of the Yellow River Basin. In this study, we developed an ecological security and comprehensive management model for the Pisha stone area. A three-year monitoring program in the Erlaohugou small watershed shows that after implementing this management model, runoff was reduced by up to 79.03% and sediment by up to 87.6%, compared to natural conditions. This study contributes to achieving the national strategic goals of ecological protection and high-quality development in the Yellow River Basin and furthering the construction of ecological civilization in China.