Recently, the intensive coastal engineerings in Yangtze River Mouth have put a serious influence on biodiversity conservation. In this region, some coastal engineerings like intertidal mudflat reclamation were undertaken in many sites. The engineering of reclamation is to build a seawall on the intertidal mudflat to stop tidal wave flowing into the enclosed area. With the disappearance of tidal wave, a series of environmental succession took place which made the environment inside seawall evolve to the terrestrial type in a short period. In addition to anthropogenic effects, these formal coastal wetlands were transformed into other forms of artificial wetlands, including rice paddies, fishing ponds, salt work, reservoirs and irrigations. In order to know whether waterbirds adapted to the great changes of environment and how the intertidal mudflat reclamation influenced the structure of waterbirds, we carried out the waterbirds survey in Nanhui Dongtan coastal area of Yangtze River Mouth from 2006 to 2010. The waterbirds was divided into three groups: shorebirds(Charadriiforms), waterfowls(Anseriformes) and egrets and herons(Anseriformes). We recorded 45 species of shorebirds, 24 of waterfowls and 15 of egrets and herons. And the dominant species were Red-necked Stint(Calidris ruficollis) in shorebirds group, Eurasian Wigeon (Anas falcate), Falcated Duck(Anas penelope) in waterfowls group, Little Egret(Egretta garzetta) and Cattle Egret(Bubulcus ibis) in egrets and herons group. The study results indicted that the shorebirds abundance declined quickly after reclamation (ANOVA, P=0.009) and waterfowls and egrets including herons increased steadily (ANOVA, P=0.015; P=0.000). However, the species diversities of shorebirds and waterfowls did not appear a significant change (ANOVA, P=0.645; P=0.523) while the species diversity of egrets and herons increases significantly (ANOVA, P=0.000). The traditional reclamation mainly destroyed natural intertidal mudflat that provides rich food resources for shorebirds forging. The loss of prefer habitat led to the sharp decrease of shorebirds abundance. But, this way might do good to waterfowls and egrets and herons. At the same time, some important species like Whistling Swan (Cygnus bewickii) and Bean Goose (Anser cygnoides) were not observed in 2009. We also investigated the occurrence frequency of representative species in different habitats from the large scale. The waterbirds habitats were classified into five types: deep water, shallow water, vegetation, mudflat and dry land. After analyzing waterbirds habitat selection and environmental factors impacting their selection with cluster analysis, we can find out the following significant correspondences between waterbirds and the key factors: the shorebirds abundance declined due to the loss of mudflat, and waterfowls, egrets and herons increased as large fish ponds with reed bed were formed after the reclamation. The recommendations about management coastal wetlands in this area have been made in our research: (1) Human disturbance should be reduced, particularly, the resident building should be avoided to develop in the surround area and tourism activity should be controlled properly; (2) Prefer habitats for shorebirds should be resorted since this area is one of the important staging sites for migratory shorebirds, and we recommend encouraging local community to develop rice paddies or ecological fish ponds rather than intensive ones to preserve some bare mudflats for shorebirds.