There are many ponds with different sizes and shapes in nature, providing a variety of ecological services. In the era of traditional farming, people created pond systems with ecological wisdom, such as Beitang ponds, multi-pond system, mulberry-based dike fish pond, etc., which perform ecological functions including water storage, stormwater regulation, pollution purification, micro-climate adjustment, and habitat provision. Due to global climate change and human interference, problems such as the surface water shortage, water pollution and water ecosystem destruction are becoming more and more serious. To deal with the changing environment, restore ecology, and construct landscape effectively, we not only could be inspired by the natural pond system, but also need to learn from the traditional cultural heritage, such as the ecological wisdom of the various pond systems. The multi-functional dike pond system plays an important role in dealing with the environmental changes and optimizing the ecological services. On the basis of clarifying the composition, structure and function of ponds in nature, this article explores the ecological wisdom of the pond systems in traditional villages, taking the design and practices of the Three Gorges Reservoir as an example to discuss the application of the multi-functional dike pond in the ecological restoration and landscape optimization of the hydro-fluctuation belt with seasonal water level fluctuation.