Microfluidic devices have been widely used to achieve highly controlled synthesis of various nanomaterials including inorganic materials, polymers and composite materials via continuous microreactors. Here, droplet-based continuous microreactors generated in a microfluidic device are used to synthesize magnetic nanoparticles (Fe3O4) via simple coprecipitation method. The chip is composed of multifunctional units, including T-junction for droplet generation, Y-junction and S-channels for droplet fusion and rapid mixing as well as the observation of the formation process of nanoparticles. The size of water-in-oil droplets was inspected by tuning the flow rate of aqueous and oil phase. By changing the temperature and flow rate of aqueous and oil streams, we investigated the variation of the morphology, size, saturation magnetization and coercivity of nanoparticles. This work presents that chemical reaction can be initiated by fusing two aqueous droplets due to the hydrodynamic coupling, which is superiorly efficient compared to the conventional coprecipitation method for synthesizing Fe3O4 nanoparticles of high saturation magnetization and low coercivity.