Long‐term carbon dioxide (CO2) flux measurements between the atmosphere and the ecosystem have been made since 1993 at a cool‐temperate deciduous forest site (Takayama) in Japan influenced by the Asian Monsoon, constituting the longest data set among all the AsiaFlux sites. Interannual variations (IAVs) and trends in the annual carbon budget components and related environmental factors were examined. Annual net ecosystem production (NEP) (mean ± 1σ) during the period of eddy covariance measurements in 1999–2021 was 265 ± 86 gC m−2 yr−1, and its IAV was dependent more on gross primary production (GPP) than on ecosystem respiration. The annual NEP and GPP were correlated with the monthly mean NEP, GPP and leaf area index from June to September, as well as with the length of the net carbon uptake period. Significantly increasing and decreasing trends in the annual NEP and GPP were detected during 2004–2013 and 2013–2021, respectively. The increasing trends were mainly caused by the vegetation recovery from typhoon disturbances. On the other hand, although the cause of the decreasing trends was not clearly identified, recent extreme weather events and/or forest succession might be related to the trends. Significant positive correlations between the start and the end of the net carbon uptake period, and between the leaf expansion and leaf fall were found. These may be attributed to phenological characteristics and negative correlation between air temperature in spring and solar radiation in early fall associated with ENSO events that can also influence IAVs in annual NEP and GPP.