In the tropical mountains of Southeast Asia, slash-and-burn (S/B) agriculture is a widely practiced and important food production system. The ecosystem carbon stock in this land-use is linked not only to the carbon exchange with the atmosphere but also with food and resource security. The objective of this study was to provide quantitative information on the land-use and ecosystem carbon stock in the region as well as to infer the impacts of alternative land-use and ecosystem management scenarios on the carbon sequestration potential at a regional scale. The study area was selected in a typical slash-and-burn region in the northern part of Laos. The chrono-sequential changes of land-use such as the relative areas of community age and cropping (C) + fallow (F) patterns were derived from the analysis of time-series satellite images. The chrono-sequential analysis showed that a consistent increase of S/B area during the past three decades and a rapid increase after 1990. Approximately 37% of the whole area was with the community age of 1–5 years, whereas 10% for 6–10 years in 2004. The ecosystem carbon stock at a regional scale was estimated by synthesizing the land-use patterns and semi-empirical carbon stock model derived from in situ measurements where the community age was used as a clue to the linkage. The ecosystem carbon stock in the region was strongly affected by the land-use patterns; the temporal average of carbon stock in 1C + 10F cycles, for example, was greater by 33 MgC ha−1 compared to that in 1C + 2F land-use pattern. The amount of carbon lost from the regional ecosystems during 1990–2004 periods was estimated to be 42 MgC ha−1. The study approach proved to be useful especially in such regions with low data-availability and accessibility. This study revealed the dynamic change of land-use and ecosystem carbon stock in the tropical mountain of Laos as affected by land-use. Results suggest the significant potential of carbon sequestration through changing land-use and ecosystem management scenarios. These quantitative estimates would be useful to better understand and manage the land-use and ecosystem carbon stock towards higher sustainability and food security in similar ecosystems