In this study, a drone-based measurement system equipped with miniaturized optical and condensation particle counters was deployed to investigate the vertical distribution of particulate matter and meteorological variables up to 2.5 km in altitude. Measurements captured at various altitudes demonstrated notable vertical variations in particle concentration and significant correlations with meteorological factors, particularly relative humidity (RH). Near the surface, within a well-mixed boundary layer, particle concentrations remained stable despite RH changes, indicating both anthropogenic and natural influences. At higher altitudes, a clear positive relationship between RH and particle number concentration emerged, particularly for smaller particles, while temperature inversions and distinct wind patterns influenced aerosol dispersion. The unmanned aerial vehicle system’s robust performance, validated against standard meteorological tower data, underscores its potential for high-resolution atmospheric profiling. These insights are crucial for understanding particle behavior in diverse atmospheric layers and have implications for refining air quality monitoring and climate models. Future work should incorporate chemical analysis of aerosols to further expand these findings and assess their environmental impact.