Honghe Nature Reserve, located in the heart of the Sanjiang Plain of Heilongjiang province, is one of the most important Nature Reserves in China and one of the largest Ramsar sites in the world. Honghe Nature Reserve was rich in biodiversity especially as waterfowl habitats supported hundreds of Red-crowned Cranes and Oriental-white Storks. But, the population of waterfowl has declined sharply since land reclamation of the area surrounding the Reserve. Conservation measures have led to the establishment of Honghe Nature Reserve to insure the persistence of habitats and population of waterfowl at a regional scale. However, little is known about the effects of landscape change of wetlands on habitats of waterfowl within the Reserve by changes to its surrounding area. This paper selected Honghe Nature Reserve and its surrounding three Farms as a research site, applying GIS techniques and habitat evaluation models to explore landscape change on wetland landscape structure of surrounding farms and its effects on habitats of Red-crowned Crane and Oriental-white Stork within Honghe Nature Reserve. Results show that: (1) Wetland area decreased 63% since intensive land reclamation occurred the farms surrounding Honghe Nature Reserve in 1983, which resulted a significant decline in wetland landscape diversity; (2) wetland landscape structure within Honghe Nature Reserve also showed significant variation, and the original high diversity landscape changed to a low diversity state, which resulted in great variation in area and spatial distribution of habitats for Red-crown Crane and Oriental-white Stork; (3) the connectivity between Honghe Nature Reserve and its surrounding farms declined to 70%, which indicates that the original matrix of wetland around Honghe Nature Reserve has been changed and the Nature Reserve has become an “isolated island” on the landscape scale, which resulted in a change in relationship between the landscape ecology of the Nature Reserve and its surrounding farm areas, especially seriously destroying the water balance between the Reserve and its surrounding areas, so the original diversity of wetland landscape types and habitat functions for waterfowl has been destroyed; (4) restoration of some areas of wetlands to their original landscape structure in the surrounding areas of Honghe Nature Reserve, to maintain the relationship of landscape ecology between the Nature reserve and its surrounding areas, is one of the best ways to effectively manage and maintain the capacity for sustainability of the Honghe Nature Reserve in the future.