Porous polymer beads (PPBs) containing hierarchical bimodal pore structure with gigapores and meso-macropores were prepared by polymerization-induced phase separation (PIPS) and emulsion-template technique in a glass capillary microfluidic device (GCMD). Fabrication procedure involved the preparation of water-in-oil emulsion by emulsifying aqueous solution into the monomer solution that contains porogen. The emulsion was added into the GCMD to fabricate the (water-in-oil)-in-water double emulsion droplets. The flow rate of the carrier continuous phase strongly influenced the formation mechanism and size of droplets. Formation mechanism transformed from dripping to jetting and size of droplets decreased from 550 μm to 250 μm with the increase in flow rate of the carrier continuous phase. The prepared droplets were initiated for polymerization by on-line UV-irradiation to form PPBs. The meso-macropores in these beads were generated by PIPS because of the presence of porogen and gigapores obtained from the emulsion-template. The pore morphology and pore size distribution of the PPBs were investigated extensively by scanning electron microscopy and mercury intrusion porosimetry (MIP). New pore morphology was formed at the edge of the beads different from traditional theory because of different osmolarities between the water phase of the emulsion and the carrier continuous phase. The morphology and proportion of bimodal pore structure can be tuned by changing the kind and amount of porogen.