It is very difficult to directly judge whether a new water conservancy project meets the requirements of ecological civilization. Based on the knowledge of engineering, archaeology, economics and history, this paper studies the ancient water control engineering by means of comparative analysis, literature review, field investigation, case study, simulation restoration and model demonstration. This paper explores the inheritance genes of water ecological civilization from three dimensions: water philosophy, engineering technology and institutional arrangements. It holds that network flow is the gene of water ecological civilization inherited by ancient water control works in China. Network flow — a flow of resources, economy, culture and value — realizes, to a great degree, the water control goals of physical grooming, economic equilibrium and ecological prudence. From the perspective of water philosophy, it displays a traditional philosophy which is systematic, prudent and dialectical. In terms of engineering technology, network flow uses astronomical-geographic information complex system to plan water sources, design structures to utilize hydro energy, regulate water quality, protect aquatic organisms, so as to form a natural-artificial water system network. In view of institutional arrangements, it constructs a hierarchical system at national, local and private levels, integrating the water conservancy practices of ancient Chinese and the essence of the traditional culture and ideology.