One of the effective means for reducing carbon dioxide emissions to mitigate global warming is by increasing carbon fixation in the ecosystem through forest management while fixing carbon by storing it in timber used for furniture or construction materials, as well as using timber as bioenergy. The study area is the Hidakagawa and the Aridagawa River catchment area. Cases of forest management comprised combinations of timber harvest cutting periods and annual thinning area ratios. We employed a forest management model BGC-ES and calculated the cumulative carbon fixation in forest ecosystem and based on timber. The simulations up to year 2100 were conducted with 2010 set as the base year. At the same time, to assess the net carbon balance, we set the demand of woody biomass. We compared the supply and demand of woody biomass for each case and analyzed the fossil fuel substitution effect derived through the use of energy as well as the cumulative carbon fixation in timber. This result suggested that generally the long rotation length is better than the short rotation cycle of forest management for the long-term viewpoint.