With the increasing awareness of environmental problems, the interest in carbon dioxide, water vapor, momentum and energy fluxes between terrestrial ecosystem and atmosphere has increased rapidly since last one or two decades. The need for measuring turbulent fluxes over different surfaces and under varying weather conditions is indispensable for the discussion of global change. Global FLUXNET and other research programs have built a large number of flux stations all over the world with using eddy covariance method as the predominant technique in the fluxes measurement and analysis. There have been now over a few hundreds of relevent measurement systems in China. Eddy covariance method seems simple. However, to obtain rather accurate and representative fluxes is dependent on many issues, particularly in difficult conditions. Eddy covariance method is a basic principle and application of atmospheric boundary layer meteorology. Compared to international progresses,there have been less relerant researches in China in recent years in such fields as the establishment of standard data processing and data quality control / quality assessment systems, and particularly the challenge for fluxes measurement in complex terrain, patched vegetation, and unfavorable meteorological conditions. A data processing system based on recommendations of FLUXNET under simpler conditions, needs to be built at first. Besides, due to more complicated (difficult) conditions in the world, there is a great need to widen the application of the eddy covariance flux measurement technique to complex surfaces. Recently, two tasks are in progress:(1) To clarify the terrain effects through careful investigation from flat to rolling terrain and to more complex landscape;(2) To better understand the flux exchange at night and week turbulence conditions by investigating “intermittent turbulence” and “flow separation” at first, for instance, at Dayekou flux station in Qilian mountain, west China.