The influences of acidic properties and pore structures of H-Beta and H-ZSM-5 zeolites on the reaction properties of n-butane isomerization at low temperatures were investigated. The results showed that bimolecular pathway of n-butane conversion predominates over H-ZSM-5 zeolites, while the monomolecular and bimolecular pathways occur simultaneously over H-Beta zeolites. The conversion rate of n-butane strongly relies on the amount of strong BrOnsted acid sites regardless of zeolite topology. However, the topology of zeolites crucially determines the products distribution, and the density of strong BrOnsted acid sites plays a secondary role. The cavities of zeolites, formed in the intersections of channels, provide the places for the bimolecular reaction. The formation of trimethyl C-8 intermediates is spatially restricted in the narrow channel intersections of H-ZSM-5 zeolites, resulting in higher contribution of n-butane disproportionation reaction. In addition, the narrow pore channels of H-ZSM-5 zeolite limit the monomolecular isomerization of n-butane molecules and affect the diffusion of heavier products (pentane) produced from bimolecular reaction, leading to the severe secondary reaction and high selectivity to propane. In contrast, the pore channels of H-Beta zeolite allow the monomolecular isomerization of n-butane and the deposition of coke.