Reducing emissions from deforestation and forest degradation in developing countries (REDD) is one of the most important carbon emission reduction efforts in the tropical region. Deforestation and land use changes are human activities with major impact on the regional carbon budged. Forest carbon biomass in Southeast Asia is largest in Asia region; however, the area of primary forest had continuously decreased due to land-use conversion. The objective of the present study was to evaluate carbon budged and greenhouse gases induced by deforestation from Borneo Island. We used time-series satellite remote-sensing data to track deforestation history in Borneo Island, Southeast Asia, and estimated the resulting forest carbon budget using a process-based model (VISIT: Vegetation Integrative SImulator for Trace gases). The model allowed us to estimate changes in carbon budged and greenhouse gases by human disturbances, including land-use conversion from primary forest to cropland (e.g., oil-palm plantation). The estimated carbon stocks, budged, and greenhouse gases were verified using field observation of previous studies at some point of Borneo Island. Our results suggested that the southern part of Borneo Island was a large carbon source due to deforestation, although the VISIT model need be revised to account for tropical peatland.