To promote Bio-Energy with Carbon dioxide Capture and Storage (BECCS), which aims to replace fossil fuels with bio energy and store carbon underground, and Reducing Emissions from Deforestation and forest Degradation (REDD+), which aims to reduce the carbon emissions produced by forest degradation, it is important to build forest management plans based on the scientific prediction of forest dynamics. For Measurement, Reporting and Verification (MRV) at an individual tree level, it is expected that techniques will be developed to support forest management via the effective monitoring of changes to individual trees. In this study, an end-to-end process was developed: (1) detecting individual trees from Unmanned Aerial Vehicle (UAV) derived digital images; (2) estimating the stand structure from crown images; (3) visualizing future carbon dynamics using a forest ecosystem process model. This process could detect 93.4% of individual trees, successfully classified two species using Convolutional Neural Network (CNN) with 83.6% accuracy and evaluated future ecosystem carbon dynamics and the source-sink balance using individual based model FORMIND. Further ideas for improving the sub-process of the end to end process were discussed. This process is expected to contribute to activities concerned with carbon management such as designing smart utilization for biomass resources and projecting scenarios for the sustainable use of ecosystem services.