The boom in dam construction and continuous river‐lake exchange has had a profound impact on the transmission and transformation of riverine dissolved inorganic carbon (DIC). An in‐depth understanding of the change mechanisms of DIC concentrations and sources driven by dam operation and lake recharge is crucial for regulating greenhouse gas emissions and evaluating the impact of DIC on the global carbon cycle. This study investigated dam‐ and lakes‐driven DIC via the concentration and δ13C of DIC, combined with anions, cations, δD and δ18O in the main stream of the Yangtze River. DIC showed a decreasing trend from upper reach (2,262.31 ± 113.69 μmol kg−1) to lower reach (1,771.61 ± 89.36 μmol kg−1). Carbonate dissolution proportion (from 36.45% to 28.44%) and atmospheric CO2 proportion (from 37.51% to 22.94%) of DIC decreased from upper reach to lower reach, whereas soil CO2 proportion of DIC (from 26.01% to 48.63%) increased. The control of dam operation on DIC biogeochemical process was revealed from different time scales. From the perspective of short‐term seasonal changes (from 2020 to 2021), the mineralization of organic matter in the dry season strengthened CO2 degassing and calcite precipitation, reducing the DIC and increasing the proportion of soil CO2. Meanwhile, longer periods of runoff retention provided sufficient time for water–rock reactions in the wet season and increased the DIC and carbonate dissolution source in the reservoir area. On a long‐term scale (from 2009 to 2021), a decrease in pH driven by sediment mineralization contributed to an annual increase in DIC in the reservoir. The flow of lakes mixed into the mainstream was revealed by the enrichment of δ18O, and river‐communicating recharge decreased the DIC and carbonate dissolution source. We show that dam operation and lake inflow change DIC concentrations and sources and therefore need to be considered in the transmission and transformation processes of DIC in the river‐ocean continuum.