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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. Plain Language Summary: Forest ecosystems play an important role in the global carbon cycle. However, time variations in the ecosystem carbon budget and responses of the ecosystems to climate change are not well understood. Although long‐term observational data are useful for a better understanding, >20‐year observations are limited, especially in the Asian monsoon region. In this study, long‐term measurements of carbon budget made at a cool‐temperate deciduous forest in Japan were analyzed for interannual variation (IAV), long‐term trends, and offered plausible causes for these changes. The IAV in annual net carbon uptake (NEP) was associated with the variation in summertime NEP, as well as with the variation in the length of the net carbon uptake period (NGP). The IAV in summertime NEP was associated with the variations in solar radiation (SR) and leaf density during the season, while the IAV in NGP depended on the variations in spring temperature and early‐fall SR. A decadal increasing trend in the annual NEP (2004–2013) was caused mainly by the recovery from typhoons, while a decreasing trend (2013–2021) may be related to recent extreme weather events and/or forest succession. Longer‐term ecosystem observations are certainly needed for more accurate predictions of forest ecosystems response to climate change. Key Points: Interannual variations and significant trends of carbon budget components at a forest site were detected from a long‐term observationThe annual carbon budget was governed by the summertime carbon uptake and the length of the growing seasonThe decadal‐scale trends of the carbon budget components obtained in this study could not have been found without the long‐term observation [ABSTRACT FROM AUTHOR]