Physical measures to control the spreading of an invasive plant Spartina alterniflora are important and necessary for biodiversity conservation at the Chongming Dongtan Nature Reserve. A field survey was carried out to trace the impact of managed waterlogging on the macrobenthic communities at the demonstration site. The results showed that managed waterlogging treatments had caused significant decreases in the density, biomass and diversity of macrobenthic community. Moreover, the community structure of macrobenthos was different drastically with the control site. After 12 month waterlogging and breaking the dike, the density, biomass and diversity of macrobenthos could recover gradually as compared with the control site. The result of multivariate analysis DCA ordination revealed that differences in community structure between the recovery site and the control site reduced gradually. The results from this study indicated that the control measure of managed waterlogging could have a negative impact on the macrobenthic community under saltmarsh vegetation, while such negative effects could be recovered by natural processes after ending the waterlogging treatment.