An effective polymeric thin film deposited by initiated chemical vapor deposition (iCVD) process was presented and its application as a barrier film on the PDMS micromold blocking the penetration of oxygen and organic solvents was investigated. With this barrier film, we were able to synthesize monodisperse polymeric particles of sizes down to 3 μm, which has been reported to be extremely challenging with bare PDMS micromold. The polymeric barrier film on the PDMS micromold enabled this successful synthesis of microparticles by effectively blocking the diffusion of oxygen, which is a well-known radical quencher in radical polymerization, through the PDMS micromold. Furthermore, the iCVD barrier film substantially decreased the penetration of various organic solvents such as acetone, tert-butanol, PDMS oil, and decane as well as organic substances including fluorescent molecules like rhodamine B and fluorescein isothiocyanate (FITC). Therefore, the polymeric barrier film coated on PDMS micromold via iCVD process will broaden the application of PDMS to microfluidic area for the synthesis of smaller microparticles with various organic substances.