Water, heat, and carbon cycle of the terrestrial ecosystems are the core of the matter and energy cycle in the land surface system. The direct measurement of land surface water, heat, and carbon fluxes at the regional scale has always been a hotspot and a gordian knot in the study of the ecosystem flux observation and simulation. Airborne eddy covariance flux measurement method can directly measure ecosystem fluxes at the regional scale. The unmanned aerial vehicle (UAV)-based eddy covariance flux measurement has the advantages of regional coverage and economy flexibility, and is the latest development direction of the airborne flux measurement method. This study firstly introduced the basic technical principle, observation characteristics, and the system construction of the UAV-based flux measurement system. Then, a comparison experiment between UAV and ground flux measurement was carried out over a typical homogeneous surface. The performance of the UAV-based flux measurement system was preliminarily evaluated by spectral analysis, fluxes comparison, and footprint analysis. The results show that the UAV-based flux measurement system could effectively sample the high-frequency turbulence signals. The turbulent fluxes measured by UAV were basically consistent with those measured from ground. However, compared with ground measurements, the UAV underestimated the sensible heat and CO₂ fluxes and overestimated the latent heat fluxes and friction velocity. The main potential reasons causing the mismatching between the UAV and ground fluxes measurements are attribute to the effects including the differences in measurement platform and instruments, vertical flux divergence, atmospheric boundary layer condition, and the differences in footprint areas as well as the influence from surface heterogeneity. At last, we proposed the future work to promote the study and the application of the UAV-based flux measurement in the relevant fields.