The modulation of triplet exciton decay in organic room-temperature phosphorescence (RTP) materials has been considered as a promising strategy for highly efficient photodynamic therapy. In this study, we report an effective approach based on microfluidic technology to manipulate the triplet exciton decay for generating highly reactive oxygen species (ROS). BQD shows strong phosphorescence upon doping into crystalline BP, indicating the high generation of triplet excitons based on the host–guest interaction. Through microfluidic technology, BP/BQD doping materials can be precisely assembled to form uniform nanoparticles with no phosphorescence but strong ROS generation. The energy decay of the long-lived triplet excitons of BP/BQD nanoparticles emitting phosphorescence has been successfully manipulated via microfluidic technology to generate 20-fold enhanced ROS than that of BP/BQD nanoparticles prepared by nanoprecipitation. The in vitro antibacterial studies indicate that BP/BQD nanoparticles have high specificity against S. aureus microorganisms with a low minimum inhibition concentration (10⁻⁷ M). BP/BQD nanoparticles below 300 nm show size-assisted antibacterial activity, demonstrated using a newly developed biophysical model. This novel microfluidic platform provides an efficient approach to convert host–guest RTP materials into photodynamic antibacterial agents and to promote the development of antibacterial agents without cytotoxicity and drug-resistance issues based on the host–guest RTP systems.