Abstract: Jiankang, as a water town in the Jiangnan area, has the Yangtze River running across its north. It is both a natural barrier and a thoroughfare. Therefore, the defense of waterways is of vital importance in the defense of its capital. The defense of the Jiankang waterways during the Six Dynasties was mainly divided into two different spatial scales:the inner city and the outer space. Inside the city, there are mainly three defense layers:the moat of the Taicheng city and the capital city, and the natural water body of the outer city wall. On the periphery, due to the dual functions of the Yangtze River as both a "natural barrier" and a "thoroughfare", the natural barrier effect led the Six Dynasties to focus on the defense of the southern bank and central bars. The function of the thoroughfare enabled the Yangtze River waterway defense area of the Six Dynasties to expand significantly from east to west, upward and downward, and controlled the intersections of the main stream and the northern and southern tributaries, thus forming barriers for the defense of the main stream of the Yangtze River. As the opposing side mainly came from upstream, two barriers were established in upstream, while only one barrier was set up in downstream, which was also protected by the sea. In terms of the spatial structure of waterway defense, due to the constraints of natural water bodies such as the Qinhuai River and the Yangtze River, as well as the internal and external city walls of the city, Jiankang City has basically formed a waterway defense structure with Taicheng as the core and multiple layers of defense. Along the Yangtze River, Jiankang is the core, and the junction area where the main stream of the Yangtze River meets the northern and southern tributaries is the checkpoint, forming a waterway defense structure with multiple barriers set up. Both natural and artificial water bodies are all influenced by natural rhythms, which makes the defense of waterways have a certain rhythm. Jiankang was able to serve as the capital of Six Dynasties for a long time, which was related to its well-developed waterway defense system.