The unique urban form on the ground and the “city overlap city” phenomenon occurring underground at Kaifeng city, on the Yellow River floodplain, is investigated. Archaeological data and historical geographical analysis were used to study the form of surface remains. Primary data were collected from four 25 m long drill cores which were obtained from different locations at Kaifeng city and the sedimentary cycles were quantitatively divided-out and dated. The results show that the evolution of Kaifeng’s surface urban form mainly occurred over four periods, the first of which was before 225 BC; the second took place between 225 BC and 956 AD; the third between 956 AD and 1219 AD; and the fourth between 1219 AD and 1907 AD. The results support the view that the city wall of today has undergone continuous reconstruction on the basis of previous city walls and thus forming the special landscape sequence of overlapped walls as a result of the 1642 AD and 1841 AD floods. The results also substantiate the “city overlap city” phenomenon at Kaifeng city where there are at least “three and a half ancient cities” located underground today, and suggests the “city overlap city” landscape is a harmonious production comprising both natural and human heritages that are of worldwide significance in terms of authenticity and integrity. Our results contribute to understanding the effects of Yellow River flooding on shaping adaptive landscapes and human beings, and suggest that Kaifeng city as well as other lower Yellow River sites become World Heritage sites.