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Thinning is a necessary procedure for the sustainable management of plantation forests. Thinning has a remarkable influence on forest carbon balance; however, there are limited studies showing the integrated assessment of the effects of thinning on several understory carbon flux components using long-term monitoring data. We measured understory flux components using automated chambers continuously over 12 years to understand the effects of forest thinning conducted in May 2014 and March 2015 and to elucidate the effect of short-term climate change on understory carbon balance in a Japanese larch (Larix kaempferi Sarg.) forest in central Japan. Although thinning (39% decrease in tree stems) increased the mean annual soil moisture by 16.5% and growing season soil temperature by 2.4%, large inter-annual variations in precipitation and soil temperature largely masked the effects of thinning on both soil respiration (R-s) and soil heterotrophic respiration (Rh). Annual mean soil temperature was positively related to all annual efflux components. Thinning also increased the understory photosynthetic photon flux density (PPFDu) by 63.1% during the growing season (May to October). In post-thinning years, the average three-year understory photosynthesis (GPP(u)), understory plant respiration (R-p), and total understory respiration (R-u) increased significantly by 59.5%, 99.7%, and 26.9%, respectively. The net understory CO2 exchange (NUE = R-u GPP(u)) changed significantly only in 2015 (13.8%). A marginally significant change in NUE based on the three-year average in post-thinning years was also detected (14.4%). Our results indicated each flux component (especially GPP(u), R-p, and R-u) changed dramatically after thinning. In contrast, the NUE of this forest was relatively more robust than other enhanced understory flux components. However, the marginally significant increase of NUE (3-year average in post-thinning years) implied a slight increase in NUE after thinning.