Portable air pollutant monitors onboard unmanned aerial systems (UAS) are increasingly being used to make vertical observations within the lower part of the troposphere. An overall evaluation of the UAS platform is critical before its wide application. To our knowledge, these evaluations have rarely been reported. This study is aimed at evaluating the performance of a fixed-wing UAS platform that is deployed with portable ozone (O3) and fine particulate matter (PM2.5) monitors. A tethered airship platform deployed with conventional O3 and PM2.5 monitors was used as a reference method to evaluate the UAS platform. To obtain custom calibration factors, the portable monitors were evaluated primarily with respect to corresponding conventional monitors at the ground level in three atmospheric environments. Then, the UAS assessment experiment was conducted over a coastal area in Shanghai, China. Seven statistical metrics were used to assess the performance of the portable monitors on the UAS platform. The results revealed that the portable monitors were capable of accurately capturing temporal variations in air pollutant concentrations after custom calibrations. The UAS platform could also accurately capture the vertical variations in O3 and PM2.5 concentrations within the lower troposphere. However, significant discrepancies between the UAS and airship platforms were observed for both O3 and PM2.5 measurements within the planetary boundary layer (PBL). The relative humidity (RH) values measured in this layer demonstrated significantly larger vertical variations and were substantially larger than those above the PBL. The discrepancies between the two platforms were associated mainly with horizontal variations in the UAS measurements over the experimental area, as well as large vertical variations in ambient temperature and RH within the lower troposphere.