The area of desert riparian Populus euphratica forest has been restored since the implementation of the ecological water transfer project in Heihe River in 2001. To support the current efforts in conservation, more knowledge is needed on energy and water exchange and its response to biophysical factors and human activities. Based on the eddy covariance technique, the processes and mechanisms of energy and water exchange were studied over the Populus euphratica forest ecosystem from 2013-2016. Results were showed as follows: (1) In the growing season, the energy consumption was dominated by latent heat flux, the value of bowen ratio was 0.21; while the energy consumption was dominated by sensible heat flux in non-growing season, the value of bowen ratio was 3.61. Irrigation events in spring and autumn made the value of latent heat flux in the early and late growth of Populus euphratica higher, which directly affected the energy partitioning. (2) The patterns of seasonal variation in evapotranspiration and latent heat flux were changed by the time of irrigation. In addition, the annual variability of evapotranspiration and latent heat flux in spring and autumn were controlled by the amount of irrigation. (3) The cumulative evapotranspiration for an entire year and growing season were estimated as 1092 mm and 932 mm, respectively. The evapotranspiration in the growing season was controlled by the system water status (irrigation events) and plant phenology.