Abstract：Since the 1990s, the Eddy Covariance (EC) system has been widely applied and has become a standard technique for quantifying exchanges of energy and matter between terrestrial ecosystems and the atmosphere. Owing to its ability to provide direct, in situ, and continuous flux measurements, it plays an irreplaceable role in global change research, land surface process modeling, and the validation and calibration of remote sensing products. This paper systematically reviews the fundamental measurement principles and the historical development of the eddy covariance technique, highlighting its theoretical basis in turbulent transport and high-frequency covariance calculations. Particular emphasis is placed on comparing the technical differences and applicable scenarios of open-path and closed-path EC systems. These differences are analyzed in terms of gas sampling methods, frequency response characteristics, environmental adaptability, and data processing procedures. Open-path systems, with their fast response, are advantageous in capturing high-frequency fluctuations, whereas closed-path systems offer better control of environmental conditions and are more suitable for harsh or variable climates. The strengths and limitations of each system are discussed in relation to specific ecosystem types and measurement objectives. In addition, the applications of both systems in measuring surface fluxes of carbon dioxide, water vapor, heat, and other trace gases are summarized, along with a detailed examination of the major sources of uncertainty, including instrumental errors, observational environmental constraints, data processing methods, as well as flux calculation errors. In recent years, the EC technique has been increasingly extended to measurements of multiple trace gas fluxes and integrated into unmanned aerial vehicle platforms, enabling observations over broader spatial scales and more heterogeneous landscapes. This development allows EC measurements to serve as an important “bridge” between ground-based observations and satellite-derived products. Nevertheless, several challenges remain, including the limited spatial representativeness of flux source areas, persistent issues with energy balance non-closure, and reduced measurement accuracy under complex terrain and extreme environmental conditions. Future developments of eddy covariance systems are expected to focus on improving measurement accuracy, enhancing data processing algorithms, expanding application domains, and advancing the development of low-power, miniaturized, and automated systems, thereby better supporting in-depth investigations of ecosystem water, heat, and carbon fluxes in the context of global environmental change.