In this study, the Taihu Lake Watershed and its level I aquatic eco-functional regions were selected as study areas, and the land use classification maps for 2005 and 2008, which were interpreted and obtained using Landsat remote sensing image, were used for further analysis. Change detection methods, e. g. transfer matrix, GIS overlay analysis, comprehensive coefficient of land use type change velocity, landscape ecological risk index and landscape ecological risk effect index of the land-use change, were selected to analyze the spatio-temporal distribution characteristics of land use and landscape as well as their transfer characteristics from 2005 to 2008 in the Taihu Lake Watershed and its level I aquatic eco-functional regions. The values of landscape ecological risk of the Taihu Lake Watershed and its level I aquatic eco-functional regions were calculated, and a comparison analysis of different characteristics of the landscape ecological risk between different level I aquatic eco-functional regions was carried out, and then the effect relationships between the landscape ecological risks and the land use changes was further analyzed. The results showed that the values of landscape ecological risk index in the eastern level I aquatic eco-functional region was bigger than that in the western level I aquatic eco-functional region both in 2005 and 2008. In 2008, compared to 2005, the value of landscape ecological risk index in the western level I aquatic eco-functional region increased by 6.49%, however, the value in eastern level I aquatic eco-functional region had a opposite change direction with a reduction of 2.57%. The comprehensive conversion rate of land use types in the eastern region was significantly 1.66 times faster than that in the western region. However, the landscape eco-risk index in the western region was -4.19 times that in the eastern region, and the response rate of landscape ecological risk to land use change in the western region was significantly higher than that in the eastern region. The reduction of landscape eco-risk index in the eastern region was mainly due to the reduction of area and patch number of lake, rural settlement, paddy field and urban landscape, and the increase of landscape eco-risk index in the western region was mainly due to the increase of area and patch number of lake, forest, urban land and rural residential landscape. Based on the above analysis, it provided a basis for the aquatic ecological protection decision-making of different aquatic eco-functional regions in Taihu Lake Watershed. And it should be focused on the land use change process and trend in the course of economic development in Taihu Lake Watershed, and the land use change direction should be properly controlled and adjusted in the region with a higher landscape eco-risk index. The management of the construction land except for the urban and rural settlements land, beaches, reservoir and pond land should be strengthened in the eastern region, and the management of the forest land, paddy field, urban land and rural residential land should be strengthened in the western region, and the appropriate-scaled land use should be introduced and the direction of land use should be kept from the high fragmentation and vulnerability, so as to reduce the landscape ecology risk and protect the landscape eco-functions in Taihu Lake Watershed.