A one-year study was carried out to investigate the seasonal fluxes and source variation of organic carbon transported by two major Chinese rivers, the Yellow River and Changjiang. In 2009, the Yellow River and Changjiang transported 3.20 × 1010g and 1.58 × 1012 g DOC and 3.89 × 1011g and 1.52 × 1012 g POC, respectively. The dominant input of the terrestrial organic matter occurred during the high discharge period from June to July for the Yellow River and from June to August for Changjiang, accounting for 36–44% of the DOC and 72–86% of the POC transported by the two rivers in 2009. The Yellow River transported much higher concentrations of inorganic carbon than organic carbon, while a reverse trend was found in the Changjiang, indicating the different sources of carbon discharged by the two rivers. Using radiocarbon and stable carbon isotope measurements, we identified the different sources and seasonal variations of organic carbon transported by the Yellow River and Changjiang. The Yellow River carried old POC with radiocarbon ages ranging from 4000 to 8000 years, while POC transported by Changjiang had a relatively younger 14C age ranging from 800 to 1060 years. The 14C ages of DOC were relatively younger (305–1570 years) and showed less variation between the two rivers. The seasonal variations found in 14C ages of DOC and POC indicate that a large fraction of recent-fixed labile organic carbon was transported by the two rivers in the spring and summer months. The different sources and seasonal variations in both fluxes and sources of organic carbon transported by the Yellow River and Changjiang could have an important influence on the biogeochemical cycle and ecosystems in the estuaries and adjacent coastal waters of the East China Sea.