Yancheng Biosphere Reserve (YBR) is located along the coastal zone of the Yellow China Sea with 900 km long in Jiangsu Province. Human activities have greatly interfered the original wetlands in YBR for migratory birds using this region as the Flyway with rapidly economic development since 1980. Much of the experimental zones and buffer zones are transferred to agriculture, aquaculture, transportation or buildings, etc. which directly results in many birds losing their habitats and becoming globally threatened, such as the Spotted Greenshank (Tringa guttifer) and the Spoon-billed Sandpiper (Eurynorhynchus pygmeus). So since 1993 some constructed wetlands have been created in the core zone of YBR in order to protect those threatened and near-threatened shorebirds. How to evaluate the sustainability of these original and constructed wetlands is a concern to managers, scientists and local stakeholders. This paper is an initial study on emergy evaluation of original wetlands and recently constructed wetlands in YBR, China. Two new emergy indices, bse emergy change (Bec) and net profit (Np), are presented in order to compare the ecological-economic benefits of these different kinds of wetlands. Results show that a waterfowl pond, constructed for ecological reasons at the edge of the core zone of YBR, has much more Bec than the original wetlands and fishponds, while its Np is negative and much lower than the other sites. Fishponds built for economic reasons in the buffer zone have negative Bec while their Np is the highest. However, the emergy yield ratio (Yr) of the original wetlands is the highest. The constructed waterfowl pond can drawmore coastal birds than before. Likewise the constructed fishponds can win large economic benefits to maintain the feedback to thewaterfowl pond. But no more fishponds should be constructed due to the highest emergy yield ratio of the original wetlands and high Bec in the waterfowl pond. Finding the best way to harmonize conservation and development in the YBR is of great importance to a sustainable future.