A microfluidc fabrication method of core shell microparticles with complex structure was reported. Microfluidic devices with different structures were assembled based on the modular analysis. The microfluidic device has advantages including low cost, easy operation and high scalability. Based on these devices, W/O/W multiple emulsion templates encapsulating inner droplets with different sizes or compositions were successfully generated. Then core shell microparticles encapsulating cores with different sizes were fabricated via UV polymerization. Moreover, alginate hydrogel was introduced to restrain the embedding materials to diffuse from cores, and core shell microparticles encapsulating cores with different compositions were also obtained. The morphology of emulsion templates and particles was observed by optical microscopy which showed narrow size distribution and uniform structure. These core shell microparticles with complicated inner structure have promising applications in fields such as drug deliver and release, microreactor, and tracer particle.