Abstract. Instrumentation packages of eddy covariance (EC) have been developed for a small unmanned aerial vehicle (UAV) to measure the turbulent fluxes of latent heat (LE), sensible heat (H), and CO2 (Fc) in the atmospheric boundary layer. This study evaluates the measurement performance of this UAV-based EC system. First, the precision (1σ) of the measurements was estimated at 0.04 m s-1 for wind velocity, 0.08 µmol m-2 s for Fc, 1.61 W m-2 for H, 0.15 W m-2 for LE, and 0.02 m s-1 for friction velocity (u*). Second, the effect of calibration parameter and aerodynamic characteristics of the UAV on the quality of the measured wind was examined by conducting a set of calibration flights. The results shown that the calibration improved the quality of measured wind field, and the influence of upwash and leverage effect can be ignored in the wind measurement. Third, data from the standard operational flights are used to assess the influence of resonance on the measurements and to test the sensitivity of the system by adding an error of ±30 % to their calibrated value. Results shown that the effect of resonance mainly affect the measurement of CO2 (~5 %). The pitch offset angle (εθ) significantly affected the measured vertical wind (~30 %) and H (~25 %). The heading offset angle (εψ) only affected the horizontal wind (~15 %), and other calibration parameters had no significant effect on the measurements. The results lend confidence to use the UAV-based EC system, and suggest future directions for optimization and development of the next generation system.