This paper examines the surface energy imbalance status over the semi-arid areas of the Loess Plateau, using the data collected by eddy covariance (EC) and boundary layer meteorological measurement systems at the Semi-Arid Climate and Environment Observatory of Lanzhou University (SACOL). The energy balance ratio is about 0.80 during the daytime in all seasons, while that is only about 0.20 in the night. For the observation time with no local circulation, the energy balance ratio is improved to more than 85% in the daytime. Even in the night of spring, summer or autumn, the energy balance ratio is also improved to 70%. However, the ratio in nighttime of winter is only 29.4%. After taking into consideration all the energy budget items, the surface energy is still not closed, which means that the eddy covariance system underestimated the turbulent heat flux. And the observation error changes with seasons, with maximum in winter and minimum in spring. The errors of sensible heat flux and latent heat flux may impact CO2 flux through the WPL correction, and cause the uncertainty of long term net ecosystem exchange (NEE), and the NEE throughout the year can be overestimated by 41.2%.