Mud flat is the typical sensitive ecological area, while its morphological feature responds to the change of sea level, the ecological structure and function also adjust to adapting to the change of coastal environment. Based on the fixed observation, sampling and analysis of the typical profile in Jiangsu coastal plain, this paper lays emphasis on discussing the principles of ecological adverse succession of mud flat caused by sea level rise. The research results show that both sea level and the phreatic water level are related to water quality, the salt content and the nutrient of soil, as well as vegetation composition and capacity of mud flat. Through not only directly increasing the frequency of tidal inundation, but also resulting in the rise in phreatic water level and increase in salinity, sea level rise will bring a series of adverse effects on ecological succession of mud flat, such as salt accumulation and decrease in nutrient of surface soil of mud flat, poor growth or degradation of vegetation and so on, till the adverse succession of the whole ecosystem, i.e., decrease in biodiversity, decline of biological capacity and ecological type tending to be single. In the study area, the imperata cylindrica var. major marsh near sea-wall will be replaced by the artemisia schrenkiana marsh due to soil salinization. Moreover, because of limitation of sea-wall, the range of imperata cylindrica var. major marsh can not expand to inland and at last will possibly disappear. The Spartina angelica swamps near the sea will become narrow because the outer part of them will gradually be replaced by bare bank and the inner part can not extend landward quickly due to the limit of its slow speed of natural reproducing, if the rate of sea level rise exceeds its natural reproducing speed, it will disappear. The artemisia schrenkiana marsh in the middle will continually expand both inward and outward, and the distribution range will gradually enlarged. The original mud flat with various ecological types will tend to be single along with sea level rise.