An analytical method for quantifying short-chain chlorinated paraffins (SCCPs) by high-resolution gas chromatography/electron capture negative ion low-resolution mass spectrometry (HRGC/ECNI-LRMS) was presented. The cleanup procedure with an acid silica gel column and activated neutral alumina column was optimized to remove the interferences. As illustration of the application of the method to environmental samples, it is found that lower chlorinated C10 and C11 compounds were the main SCCPs compounds in six sediment samples from the mouth of the Daliao River. The concentrations of SCCPs in sediments were determined to be in the range of 64.9-407.0 ng/g and showed a decreasing tendency from the shore to the remote location.