This paper mainly studied migration and transformation characteristics of dissolved organic matter (DOM) in underground aquifers. To achieve the research purpose, we carried out the dynamic column experiments of the DOM at different conditions indoors. In the experiment, the water of Wujiang River from Pingdingshan Coal-field is used as water sample, meanwhile, fine sand and marl rock are used as testing rock sample. A comparative study on migration and transformation characteristics of the DOM in different rock samples is done. The results show that, in the fine sand, the main effects are convection and dispersion, while the adsorption and biological effects are very weak. However, in the marl rock, besides existing convection and dispersion, the adsorption and biological effect are quite significant. And in the marl rock, convection and dispersion plays a major role in the early experiment, while adsorption is the main effect in the medium term, then the biodegradation dominates the final stage. With the increasing of temperature and seepage velocity in the fine sand, the impact of the convection effect becomes gradually weak, the dispersion effect gradually enhances, and, however, convection effect is still playing a dominant role. With the temperature rising in the marl rock, the adsorption effect becomes weak, but biodegradation is enhanced. As the seepage velocity increases in the marl rock, the adsorption and biodegradation both decrease.