Land use change and grassland degradation are two of the most critical problems ubiquitously found in arid and semi-arid areas in Northern China. Energy fluxes, including net radiation (R_n), latent heat flux (LE), sensible heat flux (H) and soil heat flux (G), were examined over an entire year (December 2005 to November 2006) in different steppe ecosystems – the steppe and cropland in Duolun and the fenced and grazed steppe in Xilinhot – in Inner Mongolia based on direct measurements from four eddy-covariance flux towers. The seasonal changes in R_n, LE, H and G of the four sites were similar, with very low values during the period of snow cover from December to February, followed by a gradual increase in the growing season. The opposite seasonal patterns of the LE and H fraction resulted in significant seasonal changes in Bowen ratio (β). Human activity in cropland ecosystems not only resulted in a rapidly shift between LE and H, but also triggered a decrease in latent heat fraction because of a shortened growing season of crop plants. The significantly positive relationships between canopy surface conductance (g_c) and LE/LE_eq of all of the study sites suggested that a lack of precipitation coupled with high VPD conduced remarkable decreases of stomatal conductance. This could impede the latent heat partitioning of available energy (R_n−G) in semi-arid ecosystems, Inner Mongolia. The obvious decrease in the values of g_c and the decoupling factor (Ω) in both the cropland and the degraded steppe suggested that land use change could depress latent flux fraction and increase its sensitivity to air and soil drought.