The invention discloses a system for measuring evapotranspiration of a complex ecosystem and an operating method thereof. A sensor for measuring evapotranspiration comprises a nine-needle heat pulse probe for measuring soil evaporation, a three-needle heat pulse probe for measuring the stem-flow of a plant with thick stalk and a wrapped stem-flow meter suitable for a plant with thin stalk, whereinthe nine-needle probe comprises five temperature sensing probes and four heating probes placed in a T-shaped probe handle. The invention also provides a method of estimating the evapotranspiration using the above device. The system provided by the invention has the advantages of in-situ monitoring, small disturbance to soil and vegetation, high degree of automation, convenient use, etc., and cancontinuously and automatically measure temperature changes of surface soils, soil thermal characteristics and transpiration of plants in different depths. The evapotranspiration of forest and farmlandsystems can be obtained by the invention.