Anisotropic microparticles are promising as a new class of colloidal or granular materials due to their advanced functionalities which are difficult to achieve with isotropic particles. However, synthesis of the anisotropic microparticles with a highly controlled size and shape still remains challenging, despite their intense demands. Here, we report a microfluidic approach to create uniform anisotropic microparticles using phase separation of polymer blends confined in emulsion drops. Two different polymers are homogeneously dissolved in organic solvent at low concentration, which is microfluidically emulsified to produce oil-in-water emulsion drops. As the organic solvent diffuses out, small domains are formed in the emulsion drops, which are then merged, forming only two distinct domains. After the drops are fully consolidated, uniform anisotropic microparticles with two compartments are created. The shape of the resulting microparticles is determined by combination of a pair of polymers and type of surfactant. Spherical microparticles with eccentric core and incomplete shell are prepared by consolidation of polystyrene (PS) and poly(lactic acid) (PLA), and microparticles with single crater are formed by consolidation of PS and poly(methyl methacrylate) (PMMA); both emulsions are stabilized with poly(vinyl alcohol) (PVA). With surfactants of triblock copolymer, acorn-shaped Janus microparticles are obtained by consolidating emulsion drops containing PS and PLA. This microfluidic production of anisotropic particles can be further extended to any combination of polymers and colloids to provide a variety of structural and chemical anisotropy.