Dissolved organic matter (DOM) in sediments constitutes a vital active component of the lake carbon pool. Chemodiversity of DOM groups is crucial for understanding lake carbon cycling and ecological functions. This study focused on the middle and lower reaches of the Yangtze River and Huaihe River basins, where 80 surface sediment samples were collected from 38 lakes. Using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), DOM was classified into molecular groups according to molecular compositional characteristics. We then investigated chemodiversity of different DOM groups and their driving factors under eutrophication stress. The results showed significant differences in molecular richness and composition among DOM groups. Lignin-like (39.63%) and protein-like (31.63%) compounds were the major components of sediment DOM. Their α diversity (molecular richness) was significantly higher than that of the other groups (P < 0.05), with mean values of 1125.75 and 783.73, respectively. Both groups also exhibited the lowest β diversity, as measured by Bray-Curtis dissimilarity, with mean values of 0.30 and 0.38, respectively, indicating the most uniform composition in spatial distribution. The molecular richness of most DOM groups was significantly associated with sediment physicochemical properties and land-use variables, whereas neither molecular richness nor compositional variation exhibited significant relationships with the trophic state index. Random forest analysis further quantified the relative importance of individual variables in explaining molecular richness, DOM in sediment was identified as the dominant factor for seven groups, and ammonium nitrogen (NH4+) in sediment mainly drove bioavailable groups such as carbohydrate- and amino sugar-like compounds. These results indicate that sediment physicochemical factors act as the primary drivers of molecular richness for most DOM groups. Furthermore, land-use variables such as the proportion of cropland area (Cropland%) contributed more to lignin-, tannin-, and polycyclic aromatic hydrocarbon-like groups. This may suggest that agricultural activities promote the accumulation of various recalcitrant molecules in lake sediments. Redundancy analysis showed that compositional variation in most groups was mainly explained by sediment physicochemical factors. Whereas tannin- and polycyclic aromatic hydrocarbon-like compounds were also influenced by land-use (e.g., Cropland%) and socioeconomic development (e.g., gross domestic product) factors. It indicates that natural and anthropogenic factors jointly regulate the changes of chemodiversity of DOM groups. This study enhances the understanding of chemodiversity of sediment DOM groups and their primary drivers, providing a molecular-level scientific basis for lake carbon sink management and watershed-scale carbon pool stability assessment under eutrophication.