Direct measuring of CO2 flux remains challenging for global lakes. The traditional sampling and gas transfer models used to estimate lake CO2 fluxes are variable and uncertain, and ice‐covered periods are often excluded from the annual carbon budget. Here, the first longtime (2013−2017) direct measurement of CO2 flux by eddy covariance system over the largest saline lake (Qinghai lake) in the Qinghai‐Tibet Plateau (QTP) revealed that ice‐covered period draws large amounts of CO2 from the atmosphere (−0.87 ± 0.38 g C m−2 d−1), a value more than twice the CO2 flux rate during the ice‐free period (−0.41 ± 0.35 g C m−2 d−1). The total CO2 uptake by all saline lakes on the QTP was estimated to −10.28 ± 1.65 Tg C yr−1, an equivalent to approximately one third of the net terrestrial ecosystems carbon sink in QTP. Our results indicate large sink for CO2 in winter is controlled by both seasonal hydrochemistry processes and lake ice absorption in saline lakes. This research also demonstrates decreasing CO2 uptake from the atmosphere by saline lakes on the QTP, which may turn carbon sinks to carbon sources with future warming. The first direct measurement of CO2 flux over Qinghai lake revealed that significant winter CO2 uptake by saline lakes controlled by seasonal hydrochemistry processes and lake ice absorption on the Qinghai‐Tibet Plateau (QTP). The finding highlights the importance of ice‐covered period for saline lakes in global carbon budge. All saline lakes on the QTP draw 10.28 ± 1.65 Tg C yr−1 CO2 from the atmosphere, an equivalent to approximately one‐third of the net terrestrial ecosystems carbon sink in the QTP. Increasing future climate warming may change saline lakes from carbon sinks to carbon sources by end‐2000s.