Greenhouse gases (GHGs) emissions from high-cold terrestrial ecosystems underlain by permafrost on the Qinghai–Tibet Plateau (QTP) have received widespread attention. However, the dominant factors regulating ecosystem respiration (Re) and its components (soil respiration Rs and heterotrophic respiration Rh) and how the differences in carbon emissions from different ecotypes and seasons remain are still unclear. We conducted a 2-year field investigation (August 2018 to October 2020) and applied the structural equation model (SEM) to clarify the changes in the factors controlling the respiration components during different seasons. The results indicate that the Re and its controlling factors in three alpine grassland ecosystems (alpine steppe, alpine meadow, and swamp meadow) vary with seasons. Furthermore, autotrophic respiration (Ra) contributes the most to the seasonal changes in Re. The Re gradually increases in the early growing season and rapidly decreases in the late growing season. Rh remains relatively stable during the year. Under these seasonal variations in the respiration components, the dominant factors controlling Re in the nongrowing season are the temperature of the atmosphere–soil interface (heat flux, atmospheric temperature, and soil temperature at 5 cm depth) and microbial activity (microbial carbon and pH) with the variable importance projections >1.5. During the growing season, the dominant factors regulating Re, Rs, and Rh are the soil temperature with a standardized direct effect (SDE) of 0.424, soil nutrient conditions (total nitrogen and pH) with SDEs of 0.570–0.614, and microbial activity (microbial carbon) with a SDE of 0.591, respectively. In addition, meteorological conditions have an important impact on the respiration components during the growing season. Specifically, the atmospheric vapor pressure is the dominant factor regulating the three respiration components (standardized total effects = 0.44−0.53, p < 0.001). The optimal soil water contents during the growing season (water content at which Re reaches the maximum) are 10% in the alpine steppe, 13%–15% in the alpine meadow, and 40%–43% in the swamp meadow, respectively. The effect of the soil water content on Re is more important in arid ecosystems (alpine steppe and alpine meadow) than in wet ecosystem (swamp meadow). The alleviation of water limitations in arid ecosystems may potentially increase Re.