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Understanding the effects of land cover changes on ecosystem carbon stocks is essential for ecosystem management and environmental protection, particularly in the transboundary region that has undergone marked changes. This study aimed to examine the impacts of land cover changes on ecosystem carbon stocks in the transboundary Tumen River Basin (TTRB). We extracted the spatial information from Landsat Thematic Imager (TM) and Operational Land Imager (OLI) images for the years 1990 and 2015 and obtained convincing estimates of terrestrial biomass and soil carbon stocks with the InVEST model. The results showed that forestland, cropland and built-up land increased by 57.5, 429.7 and 128.9 km 2 , respectively, while grassland, wetland and barren land declined by 24.9, 548.0 and 43.0 km 2 , respectively in the TTRB from 1990 to 2015. The total carbon stocks encompassing aboveground, belowground, soil and litter layer carbon storage pools have declined from 831.48 Tg C in 1990 to 831.42 Tg C in 2015 due to land cover changes. In detail, the carbon stocks decreased by 3.13 Tg C and 0.44 Tg C in Democratic People's Republic of Korea (North Korea) and Russia, respectively, while increased by 3.51 Tg C in China. Furthermore, economic development, and national policy accounted for most land cover changes in the TTRB. Our results imply that effective wetland and forestland protection policies among China, North Korea, and Russia are much needed for protecting the natural resources, promoting local ecosystem services and regional sustainable development in the transnational area.