Abstract: Land use changes not only affect the land structure and types, but also affect the degree of health of the land ecological system. In order to explore the ecological risks caused by the land use change, and provide scientific support for the formulation of the relevant policies and the measures, this paper described a case study on the Pearl River Delta. The characteristics of land use change were analyzed during 1990 to 2006, and the ecological risk was conducted based on the land use change, the ecological risk plots of 5km×5km were applied. Spatial distribution and gradient differentiation characters of the ecological risk in the study area were analyzed by means of spatial autocorrelation and sub-analysis of variance. The conclusions were as follows: 1) The changed land (12105.05km2) occupied 29.35% of the total land in the Pearl River Delta during 1990 to 2006. The area of construction land expanded quickly, while dike-pond increased intensively, and farmland and forests evidently decreased. Population growth, economic development, industrialization, urbanization, and the swarm of foreign investment were the main factors which led to the land use changes. 2) In 1990, the ecological risk value of the whole region was 0.2713, which increased to 0.3318; the degree of risk has increased by 22.31%. Moran's I was used to estimate the spatial autocorrelation of the ecological risks. From 1990 to 2006, the global Moran's I from 0.6451 increased to 0.7137. The spatial distribution of ecological risk showed a positive autocorrelation and significant local spatial clustering pattern. The spatial variability was primarily the result from structural factors. The high-value regions included Shenzhen, Dongguan, Guangzhou Urban District, Huadu, Nanhai, Shunde, Foshan Urban District, and Zhongshan. The changes of ecological risk in these regions were more significant, and the degree of risk increased intensively. 3) The area of high risk region and relatively high risk region expanded quickly, from 4874.52 km2 in 1990 to 12494.93 km2 in 2006, and the proportion of the total land from 11.82% to 30.30%. Meanwhile, the area of low risk region and inferior risk region decreased from 18901.54 km2 in 1990 to 13983.87 km2 in 2006, and the proportion of the total land from 45.84% to 33.91%. 4) Ecological degree of risk showed an obvious ring structure, and decreased from the axis of Foshan Urban District-Guangzhou Urban District-Shenzhen to other regions. From 1990 to 2006, the high and relatively high risk region expanded gradually from the two banks of Pearl River Estuary to the middle area of Pearl River Delta, and the degree of risk reduced gradually towards the west and the east of the Pearl River Delta. With the speeding up of the economic development and urbanization course in the Pearl River Delta, land use has intensively changed, which obviously increases land ecological risks. These conclusions can provide new ideas and methods for sustainable land use and ecological risk management, and help promote the coordination of land use and the ecological environment.