This paper reports a microfluidic method for fast continuous synthesis of Janus particles and three-phase particles with narrow size distribution. Synthesis of particles included emulsification of monomer liquids and in-situ photoinitiated polymerization of multiphase droplets. We show the strategy for precise control over the structure of Janus particles and their structure-dependent assembly in clusters. We demonstrate an asymmetric chemical modification of the surface of JPs by conjugating them with protein molecules. The Janus and ternary particles were synthesized from largely immiscible liquids and had a sharp interface between the constituent phases.