Warming will increase the carbon flux in permafrost regions, and this process may be linked with permafrost via soil hydrothermal conditions. We measured the ecosystem respiration rates (ERRs) of alpine wet meadow, alpine meadow, and alpine steppe monthly during the growing seasons in 2014 and 2016 on the northern Qinghai-Tibetan Plateau (QTP). The results showed that the temperature sensitivity (Q10) values of the ERR in alpine wet meadow and alpine meadow were higher than those in alpine steppe. The permafrost table is significantly correlated with soil temperature and moisture, thus, affects the ERRs in these ecosystems. After a 2-year warming experiment using open-top chambers (OTCs), the change rates of ERR (35.0–35.2%) were higher than those of gross primary production (GPP) (27.5–30.3%), while the absolute changes of GPP were greater than ERR. The average daytime NEE decreased by 16.5% to 21.3%, indicating more carbon assimilation was enhanced by the experimental warming. Our results show that ecosystem respiration rates in meadow and wet meadow are more sensitive to temperature increasing than those in steppe. The meadow and wet meadow ecosystems in permafrost regions on the northern QTP will assimilate more carbon than steppe in the growing seasons under climate warming scenarios.