Dissolved organic matter (DOM) plays important roles in the aquatic biogeochemical cycle and the global carbon cycle. However, it is highly spatially and temporally varied due to complex sources from the catchment (allochthonous) and from within the system (autochthonous). Satellite remote sensing provides the ability to monitor DOM and identify the spatio-temporal variations in lakes on a global or regional scale. In this study, field work was conducted in 55 lakes in August 2012 along the middle and lower reaches of the Yangtze River (MLR-YR), where most lakes were characterized by eutrophication due to intense human activities. The results showed that both colored DOM (CDOM) and total DOM differed significantly by and were linearly related to the human-induced trophic state index (TSI), with R-2 = 0.41 and 0.61, respectively. Autochthonous substances by phytoplankton contributed to 38.5% of CDOM and 35.2% of DOM, and allochthonous terrestrial substance indexed by land cover change and aquaculture contributed to almost half, with 49.7% of CDOM and 49.8% of DOM. In total, human activities explained as much as 81.7% and 87.5% of the variations in CDOM and DOM, respectively. Finally, a flowchart for estimating DOM from satellite-derived TSI was proposed. This study has great significance for synchronously monitoring and managing aquatic environment quality in regional eutrophic lakes around the world.