Under the background of rapid urban development and continuous deterioration of the ecological environment, it is an important measure to build an ecological security network to protect biodiversity. The Taihu Lake Basin is a typical trans-boundary area in China. This study takes the Taihu Lake Basin as the research area and the geospatial data from various sources as the basic data. Morphological spatial pattern analysis (MSPA), the minimum cumulative resistance model (MCR), and geospatial statistical methods, such as zoning statistics, were used.We established an ecological security model in the Taihu Lake Basin, and the structure of the ecological security model was ecological sources-moving corridors-protection network-resistance characteristics-zone regulation. The study got the following results. (1) The MSPA method was used to obtain 20 ecological sources in the Taihu Lake Basin, including large lakes and hilly forests. These ecological sources are the core areas of the Taihu Lake Basin, and they are large ecological lands, which are conducive to the protection of biodiversity in the study area. The 20 ecological sources were mainly distributed in western Zhejiang and western Taihu Lake. There are four core ecological sources in the east of Taihu Lake. (2) Gravity model was used to generate a number of important ecological corridors that run through the Taihu Lake and connected large lakes to the forest. Apart from important ecological corridors, other corridors are general ecological corridors. The general corridors are concentrated in the west of Zhejiang and Huxi area. These corridors connect the ecological sources and form an ecological network to protect biodiversity. (3) Based on the network layout of nodes, corridors, and source areas, and referring to the spatial characteristics of ecological resistance and habitat quality, including the hot spot analysis and directional analysis of the ecological resistance and habitat quality, this study constructed the ecological security pattern of "four regions and one area" in the Taihu Lake Basin. The Taihu Lake Basin has a fast economic development but a fragile ecological environment. Based on the research, this study proposes zoning control measures, which can provide a reference for the construction of the ecological network system and biodiversity protection in the Taihu Lake Basin.