To obtain a high quality bromobutyl rubber product, a higher selectivity of brominated secondary allylic structure is necessary, but it is difficult to realize in traditional reaction devices. We developed a microreaction system and used microwater droplets as an extractant to in situ remove HBr, the catalyst of the isomerization side reaction, from the organic reacting solution to prevent converting brominated secondary allyl to brominated primary allyl and degradation of the polymer chain. The microreaction system contains two micromixers, including a membrane dispersion micromixer for dispersing microwater droplets in the butyl rubber solution and a cross-junction micromixer for blending butyl rubber and Br-2 solutions. A volume adjustable delayed loop after the micromixers is used to carry out the reaction. The results show that 1 wt % water in the organic phase is satisfied to remove HBr, and 97% selectivity of brominated secondary allyl is successfully obtained under optimized operating conditions.