Colored dissolved organic matter (CDOM) is an important component of natural organic matter in water. CDOM with high concentrations may cause eutrophication of drinking water sources such as lakes and reservoirs, and even directly pollute municipal tap water. Phytoremediation is regarded as an effective, economical, and ecological method for the treatment of CDOM non-point pollution, and the purification of CDOM from wastewater treatment plant discharge. For the sake of aquatic environment protection and drinking water safety, it is very necessary to study the decolorization mechanism and environmental behavior of CDOM by plants. Through a series of experiments, the decolorization, distribution, and composition of CDOM in the rhizosphere of Phragmites austalis were investigated, as well as the influence mechanism of plant root exudates and enzyme extracting solution on the CDOM removal. The results showed that CDOM was difficult to be hydrolyzed, and its effective decolorization depended on the effect of plants. In the rhizosphere, CDOM was mainly removed by plant uptake and supplemented by root adsorption, resulting in the distribution status that most CDOM was accumulated in plants in the form of low molecule (92.2%) and the rest CDOM was adhered to root surface in the form of high molecule (7.7%). Although root exudates cannot directly affect the decolorization process of CDOM, they can enhance the carbon source utilization ability of rhizosphere microbes to the high molecular CDOM that attached on the root surface, by improving the rhizosphere microenvironment, promoting the microbial growth, enriching the related-degrading bacteria, and changing the CDOM bioavailability. Low molecular CDOM generated by biodegradation was transported into the plant through root uptake, and was further metabolized under the effect of plant enzymes, so as to achieve the purification result of CDOM by plants. The knowledges obtained from this study will be helpful to explore the decolorization mechanism and environmental behavior of CDOM in the rhizosphere, and to improve the application of phytoremediation technology for CDOM problems.