Size-controlled synthesis of MCM-49 zeolites was achieved via topology reconstruction from NaY zeolites with different sizes. SEM images showed that the sizes of the reconstructed H-MCM-49 zeolites were controlled by those of the parent NaY zeolites. Smaller NaY zeolites improved the diffusion of reactants on the parent NaY zeolites during the topology reconstruction, the final H-type zeolites, the relative crystallinity, the BET surface areas, and the number of Brønsted and total acid sites. Moreover, a substantial improvement in both ethylene conversion and ethylbenzene selectivity was observed for the H-type catalyst originating from the smaller NaY zeolite (300 nm) in liquid-phase alkylation of benzene with ethylene. This alkylation performance may provide a new strategy for enhancing both catalytic activity and product selectivity, and our method could be applicable to many diffusion-limited or external surface reactions.