Ecological integrity is a key concept in natural resource management and environmental protection and can be defined as the capacity to support and maintain a balanced, integrative, adaptive biological system, having the full range of elements and processes in the natural habitat of a region at ecosystem scale. However, ecological integrity is difficult to measure at landscape scale. A practical index of landscape integrity must provide information on the status, condition, and spatial heterogeneity of ecosystems, and it needs to include indicators of functional as well as the structural attributes. Furthermore, landscape ecology has demonstrated the importance of considering landscape context in addition to local site attributes when explaining local ecological processes and ecological integrity. The main goal of our study was to develop a landscape integrity assessment measure for wetland management and conservation in the flood plain area of Naoli Catchment that have been highly impacted by human activities at landscape scale. Based on remote sensing data and GIS techniques, we selected 10 indicators (6 for structure and 4 for function of wetlands) to constitute the landscape integrity index proposed. The conclusions showed that wetlands in the flood plain area of Naoli Catchment in 1950 had more ecological integrity than those in 2005. More human influence resulted in less ecological integrity. The riparian wetlands had the best ecological integrity than other areas in the catchment in 2005. The landscape integrity index developed here has a number of essential characteristics that make it a useful tool to assess and maintain ecological integrity, diagnose possible causes of ecological impairment, establish criteria for protecting and restoring wetland ecosystems, and integrate catchment management at landscape scale.