Optical tweezers have emerged as a powerful tool for multiparametric analysis of individual nanoparticles with single-molecule sensitivity. However, its inherent low-throughput characteristic remains a major obstacle to its applications within and beyond the laboratory. This limitation is further exacerbated when working with low concentration nanoparticle samples. Here, we present a microfluidic-based optical tweezers system that can ‘actively’ deliver nanoparticles to a designated microfluidic region for optical trapping and analysis. The active microfluidic delivery of nanoparticles results in significantly improved throughput and efficiency for optical trapping of nanoparticles. We observed a more than tenfold increase in optical trapping throughput for nanoparticles as compared to conventional systems at the same nanoparticle concentration. To demonstrate the utility of this microfluidic-based optical tweezers system, we further used back-focal plane interferometry coupled with a trapping laser for the precise quantitation of nanoparticle size without prior knowledge of the refractive index of nanoparticles. The development of this microfluidic-based active optical tweezers system thus opens the door to high-throughput multiparametric analysis of nanoparticles using precision optical traps in the future.