Water, as the source of life, plays a crucial role in life activities. It also acts as a solvent, allowing toxic and harmful substances to migrate through the water environment. In this study, an analytical method based on ion chromatography-mass spectrometry (IC-MS) is established for the direct determination of trace chlorates, perchlorates, and four xanthates in water. The Dionex IonPac AS20 chromatography column is used as the analytical column, and the CR-TC device automatically generates KOH eluent and sets up a multi-step gradient program for elution. The Dionex ADRS 600 self-circulating regeneration ion suppressor (2 mm) generates H+ through electrolysis of water, replacing metal ions in the sample solution and eluent, enabling direct tandem ion chromatography and mass spectrometry. The water sample is directly measured by IC-MS after being filtered by a hydrophilic polytetrafluoroethylene (PTFE) filter head. The results indicate that chlorate and perchlorate show good linearity in the range of 0.1–100 ng mL−1, with a quantification limit of 0.3 μg L−1. The four xanthates exhibit a good linear relationship in the range of 0.5–500 ng mL−1, and the quantification limit can be reduced to 1 μg L−1. The method offers advantages such as high recovery rate, good stability, and strong reproducibility. It shows high consistency with the results detected by the LC-MS method, but with the added benefits of being more advanced and time-saving. This innovative technology provides a new detection method for trace pollutants in water, which can aid in the prevention and control of pollutants in the water environment.