The ecological environment of watersheds has suffered from great shock and damage due to the rapid urban expansion and economic growth. This results in a trend of resource degradation, environmental degradation, disaster exacerbation, as well as the great challenge existing in ecological environment. In order to inhibit the deterioration of ecological environment and improve the human living environment, the ecological environment has been widely studied, resulting in increasing understanding of the environmental assessment. In recent years, with the transformation of environmental management goal and environmental concept, the ecological risk assessment (ERA) is becoming a key issue of ecological research as an important tool used in ecological management. During the last two decades, the study of the ecological risk assessment has been switched from biological toxicology and the effect of single chemical pollutant on environment and human health to the effect of nature disaster, the human activities (e.g., the land use, urbanization process) on the ecosystem in a large scale (e.g., the landscape, regional scales). Reference to the related research of ecological risk assessment, the paper investigates the interaction and influence mechanism among different watershed ecosystems, and assesses watershed ecological risk under the situation of multiple risk sources, risk factors, multi-endpoint and ecological receptors coexistence. Then, an index system including the hazard indicators of risk sources, the vulnerability indicators of habitats as well as the potential loss of risk receptors is build. The assessment technology system is mainly composed of comprehensive model, index system, level division and assessment unit. Finally, according to the assessment technology system build before to assess the ecological risk of Taihu Lake watershed in 2000 and 2008 using ArcGIS technologies, and then discuss the spatial-temporal evolution characteristics and the trends of ecological risk development based on the assessment results. The results show that the ecological risk values of Taihu Lake watershed range between 0.015 and 0.253, which mainly belongs to medium and low level according to the division standard of ecological risk level. The areas of higher and high level of ecological risk increased from 5.66% and 13.42% in 2000 to 6.05%, 18.42% in 2008, and number of total increasing area about 1696.13km², which mainly concentrated in the northern of watershed, such as Changzhou, Wuxi, Jiangyin City, Suzhou City, Wujiang City, Yixing City, et al. According to the characteristic of different ecological risk level areas, we put forward differentiation risk management policy to improve ecological environment and maintain the stable situation of ecological system. In addition, we also give a brief evaluation of the trend of ecological risk areas, and the corresponding suggestion to control the risk. The paper will provide decision-making support and theoretical support for watershed ecological risk and environment management.