This study demonstrates a new method for the synthesis of organic-inorganic hybrid particles composed of an inorganic silica shell and organic core particles. The organic core particles are prepared with a uniform size using droplet-based microfluidic technology. In the process of preparing the organic core particles, uniform droplets are generated by independently controlling the flow rates of the dispersed phase containing photocurable resins and the continuous phase. After the generation of droplets in a microfluidic device, the droplets are photo-polymerized as particles by ultraviolet irradiation at the ends of microfluidic channels. The core particle is coated with a nano complex composed of polyallylamine hydrochloride (PAH) and phosphate ion (Pi) through strong non-covalent interactions such as hydrogen bonding and electrostatic interaction under optimized pH conditions. The polyamine nano complex rapidly induces the condensation reaction of silicic acid through the arranged amine groups of the main chain of PAH. Therefore, this method enabled the preparation of organic-inorganic hybrid particles coated with inorganic silica nanoparticles on the organic core. Finally, we demonstrated the synthesis of organic-inorganic hybrid particles in a short time under ambient and environmentally friendly conditions, and this is applicable to the production of organic-inorganic hybrid particles having various sizes and shapes.