Ecosystem changes have an important impact on our production, life and health. The ecological cover data contains important characteristics of ecosystem changes. In order to use ecological cover data to study the spatial division and time-series changes of ecosystems, we establish the regional ecological cover change data model based on ecology data transfer matrix. Then the ecological change visual analysis system ECOVIS is designed based on the dimensionality reduction algorithm, in which the improved Sankey chart is used to realize the visualization of the ecological cover change data, the Scatter plots are designed for interactive cluster analysis, and map-based heat maps are used to display the spatial distribution of selected cluster data. The system is used to analyze the data of ecological cover in China. We analyze the time sequence of forest and town changes in local areas, and to cluster and divide the whole ecological space. The analysis results show that the method has good spatial clustering and time sequence comparison functions for the data of ecological system, which can improve the analysis of ecological cover data effectively.