The properties of bromobutyl rubber (BIIR) are closely related to its bromine content and the bonding structure of the bromine atom with the BIIR molecular chain. We here investigated the effect of these two factors on BIIR properties. We prepared BIIR with a predominant exo-methylene allyl (EXO) or endo-bromomethyl olefin (ENDO) microstructure at different levels of bromine content by controlling the conditions of bromination. BIIRs with a high bromine content had low permeability coefficients: the permeability coefficient of BIIR-3# (bromine content, 1.58 wt %) was lower than that of butyl rubber (IIR) by 23.8%. BIIRs that were predominantly ENDO with a high bromine content had a high cure reactivity and excellent compatibility with natural rubber (NR), which markedly improved the mechanical performance of the NR/BIIR blend vulcanizate. A bridge between the microstructure and macroperformance of BIIR was successfully set up, which scientifically guide for fabrication of tire inner liner with BIIR.