Inland waters serve as a critical conduit connecting the two major carbon reservoirs—land and ocean—and play a key role in the global and regional carbon cycle. China, with its vast territory spanning multiple climatic zones and hydrological regions, features complex watershed types, intense land-use changes, and significant anthropogenic disturbances, making it an ideal and representative region for studying inland water carbon cycling. To address these challenges, this study, based on the Dynamic Land Ecosystem Model (DLEM), develops a spatial representation method for hydrodynamic sub-grid processes, constructs a continuous waterbody system encompassing tributaries, main rivers, lakes, and reservoirs, enhances the spatial representation of processes in small streams and small lakes/reservoirs, and achieves dynamic simulation of biogeochemical cycles and CO₂ emissions from small water bodies. The simulation results indicate that, from 1901 to 2020, terrestrial carbon loading to China's inland waters showed an overall fluctuating upward trend, with a spatial pattern characterized by "high in the southeast and low in the northwest," and was dominated by dissolved inorganic carbon (DIC) inputs over the long term. Climate change and nitrogen input generally promoted terrestrial carbon inputs, whereas land-use change exerted an overall inhibitory effect. Carbon export from the outlets of China's inland waters exhibited significant interdecadal fluctuations and was dominated by DIC export. Climate change and land-use change generally suppressed carbon export, while the promoting effects of nitrogen input and rising atmospheric CO₂ concentration gradually intensified during the later part of the study period. These findings provide a scientific basis for deepening the understanding of carbon cycling processes in China's inland waters, improving regional carbon budget accounting, and supporting watershed eco-environmental management under the "dual carbon" goals.