Abstract: Organic pollutants are often enriched in rivers and lakes, which significantly affect human health. In this study, water samples from 18 sampling sites in the Taihu Lake basin were analyzed using a non-targeted screening method based on two-dimensional gas chromatography time-of-flight mass spectrometry (GC×GC-TOF MS). A total of 466 organic compounds were identified by the characteristic ions, accurate mass to charge ratio, retention index deviation and the NIST spectral library, of which 68 compounds were detected at more than 80% across the sampling sites, mainly attributed to flavors and fragrances products, industrial chemicals and multi-purpose compounds. Moreover, a number of compounds not yet included in the regulatory list were identified, such as cis-11-eicosanoids, dextran and gamma-sitosterol. Semi-quantitative calculations of the compounds identified by the non-targeting method revealed that the concentrations of single compound fluctuated within 0.025-113.145 μg/L. The higher concentrations were found for cis-11-eicosenamide, dibutyl phthalate and dextranol. Cluster analysis revealed that the water at the Xintang Port and Xiaomeikou sites were less polluted and were mainly influenced by emissions from the paint industry, while the remaining sampling sites were more polluted and mainly influenced by industry and food manufacturing industries. In addition, the ecological risk assessment based on the semiquantitative concentrations of 68 detected organic compounds was conducted in this study. The results indicateed that 22 pollutants were exhibited with moderate or higher ecological risk, and 11 of them were of high ecological risk, providing some references for assessing the health effects of organics in water. In summary, the non-target analysis in this study can quickly and accurately identify a large number of organics in water. Compared with the quantitative target analysis, the nontargeted analysis provides a rapid and comprehensive map for the distribution of water pollutants, which is important for determining the characteristics of the main pollutants in unknown waters and directing further analysis and assessment of water pollution.