Abstract: The growth and senescence processes of submerged aquatic macrophytes can affect the dynamic balance of dissolved organic matter (DOM) in lakes, thereby reshaping the carbon cycling patterns of lakes. To explore the impact of submerged aquatic macrophytes-based ecological restoration on lake water carbon cycling, this study focused on the submerged aquatic macrophytes restoration area and the unrestored area in Donghu Lake, Wuhan. Fourier Transform Ion Cyclotron Resonance Mass Spectrometry (FT-ICR-MS) was employed to compare the chemical diversity of DOM in the restored and unrestored areas, revealing the effects of submerged aquatic macrophytes on DOM stability in water. The results showed that submerged aquatic macrophyte plant restoration significantly improved the physicochemical properties of the water while altering the chemical diversity of DOM molecules. The restored and unrestored areas contained 7814 and 7282 types of DOM molecules, respectively. Among them, 1768 types were unique to the restored area, primarily consisting of CHO, CHON, and CHOP types, while 1236 types were unique to the unrestored area, mainly consisting of CHO and CHON types. Further analysis revealed that the restored area had 1.4 to 2.29 times more relatively recalcitrant DOM molecules containing phosphorus (CHOP, CHONP, CHOPS, and CHONPS) than the unrestored area, Additionally, the content of highly reduced DOM was higher, indicating that DOM in the restored area was more thermodynamically stable than that in the unrestored area. In summary, submerged aquatic macrophytes not only changed the composition of DOM molecules in the water but also increased the abundance of recalcitrant DOM molecules. This study enhances our understanding of the impact of lake carbon transformation processes on the carbon cycle and provides a scientific basis for accurately assessing the carbon sink potential of lakes in the future.