Traditional agriculture is overly dependent on natural conditions, which was particularly evident in the early society, and the area along the Ming-Qing old course of the Yellow River is more like a typical slice, where the contradiction between disasters and human settlements is more prominent. The area flourished on the Huai River and suffered from the floods of the Yellow River. It relied on the protection of hydraulic engineering and accommodated a large number of political immigrants. Avoiding the harm of water while pursuing the benefit of water is the way of survival for settlements and residents along the river. The development pattern and human habitat landscape model of rural settlement cluster along the Ming-Qing old course of the Yellow River are typical of the region, and their evolution process is accompanied by the transformation of the human-water relationship in rural society. The summary of development experience in diachronic research is of practical value to today’s society where floods are becoming more frequent. In recent years, the area along the old course of the Yellow River has gained new development opportunities through policies such as the ecological corridor construction, the irrigation area construction, and rural revitalization. The human habitat landscape along the old course of the Yellow River carries the culture of the ancient Huai River and the ancient Yellow River. Incorporating it into tourism can promote the integrated development of agriculture, culture and tourism. Based on the above background, taking the area along the old course of the Yellow River in Funing County as an example, the settlement cluster information and hydrological information of three historical stages (the Qing Dynasty, the Republic of China and the present-day) were restored, and ArcGIS was used to digitize and compare. The study found that water environment affected politics and military, landform and flooding, water transportation and trade, thus having a great impact on the rise and fall of settlements along the old river course. Specifically, military settlements were built near the water, residents preferred to build their settlements by dikes, and market towns emerged near waterways and ferries. Combining the above analysis, it explored the evolution of development pattern and human habitat landscape model of rural settlement cluster under the influence of water environment. The study found that the development pattern of settlements along the old river course has changed from a hierarchical and scattered individual type to a balanced and integrated overall type. The human habitat landscape model has changed from a fragmented disaster-stricken type in which settlements and flood traces are passively integrated to a stable disaster-prevention type inwhich settlements and the water conservancy system are integrated as a whole. In this process, systematic water conservancy construction has played an important role, driving the transformation of human-water relationship from seeking individual survival in floods to seeking overall development relying on water conservancy. In the early stage, regional society was in the stage of individual development. The single, decentralized and closed natural economic structure made the human habitat system highly vulnerable and unable to resist disasters. After the founding of the People’s Republic of China, systematic water conservancy projects created an integrated pattern of strip fields and water networks, which became the framework of the disaster prevention system. At the same time, it also laid an important foundation for the construction of the road network. Subsequently, the transportation mode changed from water transportation type to land transportation type, and the connections within the region and between the region and the outside world were enhanced. Systematic water conservancy construction did not only end the history of disasters along the old river course, but also promoted the transformation of rural economic development, achieved multi-objective collaborative governance, and provided a steady stream of power for the sustainable development of regional society. The three types of elements of ecology, production and life have been constructed as an organic whole, achieving the overall coordinated development of regional society. The water-adaptive human habitat landscape model along the old river course is precisely based on this development pattern. Therefore, it can be said that the development transformation and the scientific reconstruction of the human habitat system of the area along the old course of the Yellow River are the result of the joint action of top-down water conservancy construction and bottom-up settlement construction. Therefore, the development model of the area along the old river course provides a valuable template for disaster prevention and sustainable development of regional rural society.