Airborne Eddy Covariance (EC) method is one of the most effective ways to measure the turbulent fluxes over regional scale directly. The turbulent fluxes from airborne EC method have the same spatial scale with the pixel scale of remote sensing image and the grid scale of land-surface models, which is very important for the simulation of regional or global land-surface fluxes. UAV-based eddy covariance method could achieve the observation of turbulent fluxes in a multi-period and multi-sorties way, and the observation result is reliable and the application is inexpensive. It is an important development direction for airborne flux observation technique. After the introduction of the main technical characteristics of the airborne EC method, this paper reviewed the worldwide progress in UAV-based fluxes measurements system from these aspects of the specifications of the UAVs, the integrated instruments, and the analysis of the application cases. Then, the main sources of uncertainty affecting the UAV-based fluxes measurements were discussed. At last, the shortcomings of the current UAV-based flux observation system were summarized. A brief outlook about UAV-based fluxes measurements technique was also given.