Accelerator mass spectrometry is the only method for measuring 129I in low level environmental samples. In this method, it is essential to convert organic associated iodine into inorganic form for the determination of total 129I or organic 129I because AgI is usually adopted as a target for AMS measurement of 129I. The chemical oxidative method to release iodine from organic matter in natural water was investigated using anion exchange chromatography and CHCl3 extraction methods. K2S2O8 was confirmed to be an ideal oxidative reagent for decomposing organic matters and converting organic iodine to inorganic form. More than 95% of iodine in natural water can be separated by solvent extraction after oxidation under optimal conditions, and the isotopic exchange of iodine in inorganic and organic forms was well completed during the oxidation, being able to result in an identical 129I/127I ratio as in the original water. Our works indicate that the reported chemical oxidation method is a suitable approach for releasing organic associated iodine in natural water to allow separation of iodine and preparation of the AgI target for AMS measurement.