Airborne eddy covariance (EC) measurement is one of the most effective methods to directly measure the surface mass and energy fluxes at the regional scale. It offers the possibility to bridge the scale gap between local- and global-scale measurements by ground-based sites and remote-sensing instrumentations, and to validate the surface fluxes estimated by satellite products or process-based models. In this study, we developed an unmanned aerial vehicle (UAV)-based EC system that can be operated to measure the turbulent fluxes in carbon dioxides, momentum, latent and sensible heat, as well as net radiation and photosynthetically active radiation. Flight tests of the developed UAV-based EC system over land were conducted in October 2020 in Inner Mongolia, China. The in-flight calibration was firstly conducted to correct the mounting error. Then, three flight comparison tests were performed, and we compared the measurement with those from a ground tower. The results, along with power spectral comparison and consideration of the differing measurement strategies indicate that the system can resolve the turbulent fluxes in the encountered measurement condition. Lastly, the challenges of the UAV-based EC method were discussed, and potential improvements with further development were explored. The results of this paper reveal the considerable potential of the UAV-based EC method for land surface process studies.