A molecular dynamics study has been carried out on the diffusion of trimethylbenzene (TMB), toluene, and xylene molecules in transalkylation of TMB and toluene in UWY zeolite, containing crossing 10-ring and 12-ring channels. Two models of UWY have been employed, the pure silica and an acidic form of UWY including Al and Brønsted sites, using a recently parameterized general force field for zeotypes, which reproduce pore diameters within ca. ±0.2 Å. Molecular traffic has been observed from the result of TMBs using almost exclusively the 12-ring channels and the preferential location of p-xylene and toluene in the 10-ring channels at high loading (reaction conditions). From the three different 10-ring channels, only p-xylene and toluene can fit in the two smallest channels, whereas m-xylene and 1,2,4-TMB can also diffuse in the largest 10-ring channel. An in-depth analysis of transition-state shape selectivity has been performed, showing that all transition states of transalkylation of toluene and TMBs can be formed in the 12-ring channels. Although this is a disadvantage for the selective production of p-xylene, the previous factor of molecular traffic will contribute to a selectivity of p-xylene over the other xylene isomers. Overall, UWY is suggested as a promising catalyst for transalkylation of toluene and TMBs.