In this study, we present an integrated microfluidic-based ultrafine water condensation particle counter (UWCPC) developed by innovatively combining lab-on-printed circuit board (PCB) and three-dimensional (3D)-printing technologies. The combined lab-on-PCB and 3D-printing technology used for UWCPC development is an optimized method for manufacturing low-cost miniaturized integrated microfluidic devices. Notably, high-precision, harmless nanoparticle measurements were realized using a sheath/sample air separator and a moderated water condensation method. This novel methodology provides a highly accurate, harmless, low-cost, miniaturized system for multipoint monitoring of airborne nanoparticle generation and growth mechanisms. Our system consisted of three main parts—a sample/sheath air separator, a nanoparticle growth sector, and a miniaturized optical particle counter (OPC)—and was rigorously evaluated using simulations to confirm its optimal design and performance. The nanoparticle growth sector consisted of PCBs and 3D-printed structures; the heater, various sensors, and super hydrophilic micro-pillar array wick necessary for nanoparticle growth were integrated on the PCBs. Through quantitative laboratory experiments, we determined that our system was capable of counting particles 3.4 nm in diameter. In addition, the role and effect of the sheath air were confirmed by measuring the particle counting efficiency according to the ratio of the sample and sheath air. Finally, high concordance was confirmed through one-to-one comparison with a reference aerosol instrument in a wide particle number concentration range (0–57 000 N cm⁻³). Accordingly, if sufficient field tests in the environment confirm the practical use of the developed UWCPC, the generation and growth mechanism of nanoparticles in the air can be monitored.