Due to the vast wetlands and associated rich biodiversity, Central Yangtze river and its lakes basin (i.e. Central Yangtze Ecoregion) is designated by WWF as one of the Global 200 Ecoregions that contains a distinct assemblage of natural communities sharing a large majority of species, dynamics, and environmental conditions, and effectively functioning as a conservation unit. However, in the past half century the wetlands in the Central Yangtze and the biodiversity they support have suffered from constant threats, mostly associated with human activities, such as large-scale agricultural practices, land reclamation, water projects building and rapid urbanization, etc. This article therefore aimed at establishing and optimizing ecological network for wetland conservation in the Central Yangtze Ecoregion based on Gap analysis. To conduct Gap analysis, a comprehensive spatial dataset was established based on different factor combinations of landform, vegetation and landcover types, and the habitat suitability classes were defined with the analysis on the distribution area and habitat requirements of focal waterbirds (i.e. Grus leucogeranus, Ciconia boyciana, Anser erythropus and Mergus squamatus) in the Central Yangtze Ecoregion. Habitat suitability unit was used to identify regional potential habitats through spatial extrapolation with GIS dataset in which a spatial linkage between the species distribution and main eco-geographic factors were built. Comparing the potential habitats with existing distribution of wetland nature reserve in the Central Yangtze Ecoregion, the Gaps (i.e hotspots of species while not included in the existing conservation system) of wetland conservation in the Central Yangtze Ecoregion were located, and conservation efficacy of existing conservation system thus was evaluated. Given the integrity and connectivity of existing conservation system, an optimized wetland conservation network was finally developed from the Gap analysis and spatial patterns of existing conservation network. The results showed that, the potential habitats of focal species cover 134 counties in the Central Yangtze Ecoregion, but only 23.5% of the total area of the potential habitat has been included into the existing conservation system in 23 counties. Lots of potential habitats are still directly exposed to the human impacts. To improve and optimize the spatial pattern of existing wetland conservation system in the Central Yangtze Ecoregion, it is necessary to establish new wetland nature reserves in 22 counties across Hubei (15counties), Anhui (9 counties) and Jiangxi (1county) provinces. These proposed protected areas should be well integrated with existing conservation system, thus it can form a larger and optimized conservation network system composed of 45 counties and provide an effective wetland conservation system in the Central Yangtze Ecoregion. The results also demonstrated that it would be applicable to introduce concept of Habitat Suitability Unit (HSU) in macro-scale habitat analysis with assistance of GIS-based eco-geographic dataset.