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 technology for the treatment of CDOM non-point pollution, and the purification of CDOM polluted wastewater treatment plant discharge. For the sake of aquatic environmental protection and drinking water safety, it is very necessary to study the decolorization mechanism and environmental behavior of CDOM by plants. In the present study, the decolorization, distribution, and composition of CDOM in the rhizosphere of Phragmites australis 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, forming the distribution characteristics that most of the CDOM were accumulated by plants as low molecules (92.2%) and the rest were adhered to root surface as high molecules (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, by improving the rhizosphere microenvironment, promoting the microbial growth, enriching the related-degrading bacteria, and changing the CDOM bioavailability. Low molecular CDOM generated by microbial degradation was transported into the plant through root uptake, and then were metabolized under the effect of plant enzymes, so as to achieve the purpose of CDOM purification by plants.