The study of the surface energy balance characteristics of different ecosystems in the Qinghai Plateau is of great significance for a deeper understanding of land surface processes, the water cycle, and global climate change. This study aims to compare the seasonal variations in energy balance and partitioning of four typical ecosystems on the Qinghai Plateau—swamp meadows, subalpine mountain meadows, alpine shrublands, and alpine deserts. Mantel analysis and path analysis were used to explore the regulatory mechanisms of meteorological elements on energy fluxes and the Bowen ratio (β). The results showed the following: (1) Net radiation (Rn), sensible heat flux (H), and latent heat flux (LE) all exhibited a single-peak pattern of change, and the energy partitioning was closely related to the hydrothermal conditions. Swamp meadows and subalpine mountain meadows were dominated by LE throughout the year and the growing season, while H dominated in the non-growing season. Meanwhile, alpine shrublands and alpine deserts were dominated by H throughout the year. (2) β reflected the characteristics of turbulent fluxes variations and the moisture level of the underlying surface. Swamp meadows and subalpine mountain meadows were relatively moist, with the value of β all being less than 1. Alpine shrublands and deserts were comparatively arid, with the values of β all exceeding 1. The energy closure rate ranged from 48% to 90%, with better energy closure conditions observed during the growing season compared to the non-growing season. (3) Meteorological factors collectively regulated the variations in energy fluxes and its partitioning, with H and LE being primarily influenced by Rn, relative humidity (RH), and soil moisture (Ms). β was significantly affected by RH, Ms, and the saturated vapor pressure deficit (VPD). The sensitivity of the ecosystems to changes in fluxes increased with decreasing moisture, especially in alpine deserts, with Ms, VPD and RH being the most affected. Swamp meadows were significantly associated with air temperature (Ta), soil temperature (Ts), and wind speed; subalpine mountain meadows with Ta and Ts; and alpine shrublands with Ta. These results provided a basis for further analyses of the energy balance characteristics and partitioning differences of different ecosystems on the Qinghai Plateau.