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Instrumentation packages for eddy covariance (EC) measurements have been developed for unoccupied aerial vehicles (UAVs) to measure the turbulent fluxes of latent heat (LE), sensible heat (H), and CO2 (Fc) in the atmospheric boundary layer. This study aims to evaluate the performance of this UAV-based EC system. First, the measurement precision (1σ) of georeferenced wind was estimated to be 0.07 ms-1. Then, the effect of the calibration parameter and aerodynamic characteristics of the UAV on wind measurement was examined by conducting a set of calibration flights. The results showed that the calibration improved the quality of the measured wind field, and the influence of upwash and the leverage effect can be ignored in wind measurement by the UAV. Third, for the measurements of turbulent fluxes, the error caused by instrumental noise was estimated to be 0.03 µmolm-2s-1 for Fc , 0.02 Wm-2 for H , and 0.08 Wm-2 for LE. Fourth, data from the standard operational flights were used to assess the influence of resonance on the measurements and to test the sensitivity of the measurement under the variation (±30 %) in the calibration parameters around their optimum value. The results showed that the effect of resonance mainly affected the measurement of CO2 (∼5 %). The pitch offset angle (εθ) significantly affected the measurement of vertical wind (∼30 %) and turbulent fluxes (∼15 %). The heading offset angle (εψ) mainly affected the measurement of horizontal wind (∼15 %), and other calibration parameters had no significant effect on the measurements. The results lend confidence to the use of the UAV-based EC system and suggest future improvements for the optimization of the next-generation system. [ABSTRACT FROM AUTHOR]