Exploring the surface energy exchange between atmosphere and water bodies is essential to gain a quantitative understanding of regional climate change, especially for the lakes in the desert. In this study, measurements of energy flux and water vapor were performed over a lake in the Badain Jaran Desert, China from March 2012 to March 2013. The studied lake had about a 2-month frozen period (December and January) and a 10-month open-water period (February-November). Latent heat flux (LE) and sensible heat flux (Hs) acquired using the eddy covariance technique were argued by measurements of longwave and shortwave radiation. Both fluxes of longwave and shortwave radiation showed seasonal dynamics and daily fluctuations during the study period. The reflected solar radiation was much higher in winter than in other seasons. LE exhibited diurnal and seasonal variations. On a daily scale, LE was low in the morning and peaked in the afternoon. From spring (April) to winter (January), the diurnal amplitude of LE decreased slowly. LE was the dominant heat flux throughout the year and consumed most of the energy from the lake. Generally speaking, LE was mostly affected by changes in the ambient wind speed, while Hs was primarily affected by the product of water-air temperature difference and wind speed. The diurnal LE and Hs were negatively correlated in the open-water period. The variations in Hs and LE over the lake were differed from those on the nearby land surface. The mean evaporation rate on the lake was about 4.0 mm/d over the entire year, and the cumulative annual evaporation rate was 1445 mm/a. The cumulative annual evaporation was 10 times larger than the cumulative annual precipitation. Furthermore, the average evaporation rates over the frozen period and open-water period were approximately 0.6 and 5.0 mm/d, respectively. These results can be used to analyze the water balance and quantify the source of lake water in the Badain Jaran Desert.