In this study, organic compounds were screened in surface water collected from Xujiahe basin, China by gas chromatography-mass spectrometry (GC–MS). A total of 51 compounds were identified including 14 organochlorine pesticides (OCPs), 9 organophosphorus pesticides (OPs), 16 polycyclic aromatic hydrocarbons (PAHs) and 12 chlorobenzene (CBs). The concentrations of OCPs, PAHs and CBs were generally low. The concentrations of OCPs in Xujiahe reservoir ranged from N.D. to 35.6 ng/L, the concentrations of PAHs ranged from N.D. to 19.8 ng/L and the concentrations of CBs ranged from 10.3 to 124.6 ng/L. The Ecological Structure Activity Relationships (ECOSAR) model was employed to directly predict the integrated toxicity indexes of 51 organic pollutants. The risk quotient (RQ) values of most of the organic compounds in the water samples were acceptable for their ecological risk.