The adsorption of toluene and 1,3,5-trimethylbenzene and the catalytic transformation of 1,3,5-trimethylbenzene are applied as probing approaches to characterize the pore system of hierarchical EU-1 zeolites prepared using organofunctionalized fumed silica as the silicon source. The adsorption and diffusion of toluene and 1,3,5-trimethylbenzene are significantly improved in the hierarchical EU-1 zeolites compared with the conventional microporous EU-1 zeolite. The adsorption kinetics of toluene and 1,3,5-trimethylbenzene suggested that introducing mesopores significantly increases the rate of adsorption and improved the diffusion of large molecules. In the catalytic transformation of 1,3,5-trimethylbenzene, the conversion of 1,3,5-trimethylbenzene on the hierarchical EU-1 zeolites is doubled compared with the conventional microporous EU-1 zeolite, due to the improved diffusion of bulky molecules and enhanced accessibility of active sites in the hierarchical EU-1 structure. Although isomerization is the main reaction, differences are observed in the product ratios of isomerization to disproportionation between the hierarchical EU-1 zeolites and the microporous counterpart with different times on stream. The transformation of 1,3,5-trimethylbenzene over the hierarchical EU-1 zeolites has a higher isomerization to disproportionation ratio than that over the microporous EU-1 zeolite; this is due to the increased mesoporosity.