This chapter reports research on Japanese terrestrial natural ecosystems from the Climate Change Adaptation Research Program by the National Institute for Environmental Studies. We detected colder juvenile shifts compared to adults of the same species, suggesting past colder shifts of forest tree species. We assessed the vulnerability of forest tree biodiversity against future climate change using national forest inventory data and the Info-gap decision theory. Regional fine-scale vegetation shifts were projected and evaluated in the Mt. Taisetsu region using vegetation maps, species distribution models, and a decision-supportive SecSel model. We then summarized candidate refugia habitats and realistic target intervention sites for the use of ecosystem service and management of vegetation. These methodologies are applicable to other regions and would help approach complex ecological mechanisms behind and create better decisions to adapt to future climate conditions. We hope this report further provides positive stimulations to other research fields, connecting them and approaching generalized climate change adaptation.