Sorption is one of the main mechanisms by which montmorillonite is used in water pollution treatment. In this study, montmorillonite was used to adsorb phenolic pollutants in wastewater and to study the adsorption mechanism of the process. The sorption was analyzed for surfactants (CTMA+) and different pollutants (phenol/2-naphthol). It was found that in the aqueous environment, water molecules had some influence on the arrangement of the components including modifiers, inorganic cations and contaminants, and the above components were slightly more active than in the dry state. The modifiers arrangement shifted from a laminar to a tilted distribution with the increase of loading amount, and the main sorption sites for organic pollutants were shifted from the inner surface of organo-montmorillonite to the organic phase in the organo-montmorillonite. The free binding energy of phenol under MMT-1.0 loading is − 211.780, which is slightly lower than − 207.066 and − 204.147 under MMT-1.75 and MMT-0.25 loading. When 2-naphthol is used, the free binding energy of MMT-1.0 reaches − 343.38, which is much lower than that of − 272.51 and − 217.92 under the loading of MMT-0.25 and MMT-1.75, indicating that the adsorption effect of organic matter under the loading of MMT-1.0 is better and the adsorption effect of montmorillonite on 2-naphthol is stronger than that of phenol.