The terrestrial ecosystems of Qinghai-Tibet Plateau (QTP) are highly sensitive to climate change, yet the magnitude and distribution of the carbon budget for QTP remain quite uncertain. Here, utilizing long short-term memory networks (LSTM), in conjunction with available eddy covariance flux data from recent extensive observation campaigns, multiple satellite land surface data, and observation-based environmental data (e.g., soil organic carbon, SOC), we revisit the regional carbon budget estimation over the QTP with a special focus on investigating the impacts of considering memory effect and incorporating SOC. Our estimate points the QTP region to a mean carbon sink of 20.89 Tg C yr-1 during 2003–2018. Spatially, the major sinks distribute in the western and northern QTP dominated by alpine steppes, while major sources in the eastern QTP dominated by alpine meadows. During the study period, the regional sink declines at the rate of 0.0003 Tg C yr-2, which is primarily contributed by the reduced carbon sink of alpine steppes and the increased carbon source of alpine meadows. We found that considering memory effect and incorporating SOC are critical for estimating the regional carbon budget for QTP. Without considering memory effect leads to a huge carbon source of 161.10 Tg C yr-1, with unreasonable seasonal and interannual variation of carbon budgets. Without incorporating SOC leads to a larger estimated carbon sink (61.94 Tg C yr-1), with clearly overestimated sink in steppes ecosystems and underestimated source in meadows ecosystems. Our study provides new insights into the carbon budget estimation for the QTP region.