In this study, the natural evolution and human disturbance of interconnected river system networks in the nearly one the thousand years in Huai River Basin were analyzed, and the causes were discussed. Furthermore, some urgent resolved scientific questions were proposed. The results showed that: the current interconnected river system was the integrated flooding control, drainage, irrigation, and water supply system which was formed during the long-term struggling against the flooding and sediment of Yellow River. It obeyed the natural rules and considered the development of soc-economy. The main rivers and tributaries were regulated by human activites, the natural-artificial river networks were anastomatic, the water exchange between rivers and lakes was frequent, and the sea-entryway and Yangtze-entryway was straightway, the river systems were interconnected with Yellow River, Yangtze River and Hai River. The interconnected river system networks pattern resolved the problems that the flooding had no way to sea and the floods happened frequently. The river system networks promoted the economy development and the society unity in Huai River Basin, but also brought a certain negative impact on ecosystem and environment. The studies on the water resource variation, the eco-environmental and soc-economic pattern influences under the impact of interconnected river system were some urgent resolved scientific questions in current interconnected river system networks.