We report a simple process to fabricate monodisperse tetra-arm poly(ethylene glycol) (tetra-PEG) hydrogel microcapsules with an aqueous core and a semipermeable hydrogel shell through the formation of aqueous two-phase system (ATPS) droplets consisting of a dextran-rich core and a tetra-PEG macromonomer-rich shell, followed by a spontaneous cross-end coupling reaction of tetra-PEG macromonomers in the shell. Different from conventional techniques, this process enables for the continuous production of hydrogel microcapsules from water-in-oil emulsion droplets under mild conditions in the absence of radical initiators and external stimuli such as heating and ultraviolet light irradiation. We find that rapid cross-end coupling reaction of tetra-PEG macromonomers in ATPS droplets in the range of pH from 7.4 to 7.8 gives hydrogel microcapsules with a kinetically arrested core-shell structure. The diameter and core-shell ratio of the microcapsules can be easily controlled by adjusting flow rates and ATPS compositions. On the other hand, the slow cross-end coupling reaction of tetra-PEG macromonomers in ATPS droplets at pH 7.0 and lower induces structural change from core-shell to Janus during the reaction, which eventually forms hydrogel microparticles with a thermodynamically stable crescent structure. We believe that these hydrogel microparticles with controlled structures can be used in biomedical fields such as cell encapsulation, biosensors, and drug delivery carriers for sensitive biomolecules.