Heterogeneous hydrogenation is surging as a promising strategy for selective removal of water pollutants, yet numerous efforts rely on catalyst design to advance catalytic activity. Herein, we enhanced the mass transfer and the utilization of hydrogen reagent through construction of a two-phase flow-through membrane reaction device (Pd/SiC-MR). Pd/SiC-MR displays high efficiency and selectivity toward removal of multiple pollutants. For instance, rapid (∼0.35 s) and exclusive hydrogenation (>99%) of carbon-chlorine bond in organohalogens were realized at high water flux (220 L/m2/h). More importantly, the two-phase Pd/SiC-MR reaction system achieved 31.4% utilization of hydrogen reagent, 1-3 orders of magnitude higher than those by classical slurry or fixed-bed reactor. The high hydrogenation performance is attributed to the close proximity of the hydrogen source, reactive hydrogen atom, and pollutant under high molecular collision frequency in membrane pores. Our study opens an approach for improved hydrogen reagent utilization while reserving the high pollutant removal efficiency through altering operating conditions, beyond complex material design limitations in hydrogenation water purification.