Tropical cyclones (“typhoons”) affect ecosystem processes by disturbing the ecosystem's biogeochemistry, population dynamics, and services. The impact of 10 typhoons that struck the Japanese Islands in 2004 was studied using a process-based ecosystem model (Vegetation Integrative SImulator for Trace gases) and by interpreting deviations in the carbon budget observed at the Takayama forest site in central Japan. The site-calibrated model appropriately simulated gross and net CO2 fluxes in most years but could not capture the clear depression of CO2 uptake in 2004, probably because it neglected the impact of defoliation on the canopy's carbon gain due to strong typhoon winds. The defoliation intensity caused by each typhoon event was inversely estimated from the flux measurement data and using a Monte Carlo approach. Accounting for the repeated 10%–20% defoliation that occurred in 2004 lowered the canopy carbon gain by nearly 200 g C m−2 yr−1, resulting in better agreement between the estimated and observed flux values. Comparison of the estimated defoliation pattern with satellite-based estimates of leaf area index indicated that such moderate defoliation from midsummer to autumn was plausible. The influence of CO2 emissions from typhoon-generated debris on the carbon budget in subsequent years was estimated to be tiny in this case. These results have implications for regional carbon accounting studies, because both devastating and moderate defoliation caused by tropical cyclones can have a marked effect on the regional carbon budget, especially when defoliation occurs repeatedly within a single growing season.