The elimination mechanisms and the dynamics of 2,5-dimethylbenzoquinone/2,6-dimethylbenzoquinone are performed by DFT under the presence of ·OH radical and TiO2-clusters. The rate coefficients, calculated within the atmospheric and combustion temperature range of 200–2000 K, agree well with the experimental data. The subsequent reactions including the bond cleavage of quinone ring, O2 addition or abstraction, the reactions of peroxy radical with NO yielding the precursor of organic aerosol are studied. Gaseous water molecule plays an important role in the transformation of alkoxy radical and exhibits a catalytic performance in the enol-ketone tautomerism. The lifetimes of 2,5-dimethylbenzoquinone/2,6-dimethylbenzoquinone are about 12.04–12.86 h at 298 K, which are in favor of the medium range transport of them in the atmosphere. Significantly, the water environment plays a negative role on the ·OH-degradation of dimethylbenzoquinone. Compared to the quinone ring, 2,5-dimethylbenzoquinone onto (TiO2)n clusters (n = 1–6) is easier to be absorbed by TiO2-clusters through its oxygen site because of its strong chemisorption, which indicates that TiO2-clusters are capable of trapping dimethylbenzoquinones effectively. The water environment could weaken the adsorption of 2,5-dimethylbenzoquinone onto (TiO2)n clusters (n = 1–6) by increasing the adsorption energy. This work reveals the removal of dimethylbenzoquinones and the formation of organic aerosol under polluted environments.