The optimization of installation of baffles in a UV rector is investigated. The flow field is obtained by solving continuity and momentum equations. The radiation intensity is solved by a radiative transfer equation. The UV dosage is obtained by coupling the Lagrangian particle tracking approach with the solved radiation intensity. One unbaffled reactor and two baffled reactors are simulated. The baffled UV reactor A has the longest residence time and the lowest UV dosage while the baffled UV reactor B has the relatively longer residence time and the highest UV dosage. The unbaffled reactor performs between the two baffled reactors considering residence time and UV dosage. The baffled UV reactor B enables the best disinfection of microorganisms. The results demonstrate that optimization should consider flow field and radiation intensity simultaneously.