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Energy flux is a key component and driving factor in ecosystem processes and functions. Using 2015 datasets of eddy covariance, vegetation and meteorological measurements at four dominant ecosystems on the Mongolian Plateau, we analyzed the inter-site and seasonal variations and underlying biophysical controls on energy balance and partitioning in a meadow steppe (MDW), typical steppe (TPL), dry typical steppe (DRT) and shrubland (SHB). Vegetation dynamics dominated the energy partitioning. The growing season (May-Sept) net radiation (Rn) was 20% less at SHB due to higher bare soil coverage area than that at MDW. High vegetation cover and soil water content resulted in the highest latent heat (LE) at MDW, while sparse vegetation showed the highest sensible heat (H) at DRT among the four vegetation types. The Bowen ratios (β, H/LE) at TPL (1.68), DRT (1.44) and SHB (1.44) were an order of magnitude higher than that at MDW (0.14). At DRT and SHB, β had significantly negative feedback on canopy conductance (p < 0.05) and significantly positive feedback on vapor pressure deficit (VPD) (p < 0.05). We emphasized that the complex, interactive effects of vegetation types, ecosystem structures, and microclimate for the energy balance and partitioning.