Abstract: In order to determine the ground datum construction elevation of the new urban area of plain river network, this paper took the Lianhu new town catchment area of Danyang City, Jangsu Province as the research object. On the premise of meeting the flood control standard of a 50-year flood, the influence of high and low flood water level control schemes before flood season on the maximum design water level and site vertical scheme was studied by MIKE 11 hydrodynamic model and cut/fill module of ArcGIS software. And then the two schemes were compared from four aspects: safety guarantee, earthwork balance, excavation and filling area and harmony water-human relation. The results showed that both two schemes can ensure the safety of drainage, but compared with the high water level control scheme, the low water level control scheme was more suitable for the construction elevation of Lianhu new town due to its lower maximum water level control, delayed peak time, smaller earthwork gap, and smaller excavation and filling area. Through the coupling analysis on the highest water level control of urban water system and the vertical elevation of the site, it can provide a reference for the determination of the vertical datum elevation of new towns’ construction in the southern plain area of China.