Low-molecular-weight (LMW, <1000 Da) dissolved organic matter (DOM) plays a significant role in metal/organic pollutant complexation, as well as photochemical/microbiological processes in freshwater ecosystems. The micro size and high reactivity of LMW-DOM hinder its precise characterization. In this study, Suwannee River fulvic acid (SRFA), a commonly used reference material for aquatic DOM, was applied to examine the optical features and molecular composition of LMW-DOM by combining membrane separation, ultraviolet–visible absorption and Orbitrap mass spectrometry (MS) characterization. The 100–500 Da molecular weight cut-off (MWCO) membrane had a better performance in regard to separating the tested LMW-DOM relative to the 500–1000 Da MWCO membrane. The ultraviolet–visible absorbance decreased dramatically for the retentates, whereas it increased for the dialysates. Specifically, carbohydrates, lipids and peptides exhibited high selectivity to the 100–500 Da MWCO membrane in early dialysis. Lignins, tannins and condensed aromatic molecules displayed high permeability to the 500–1000 Da MWCO membrane in late dialysis. Overall, the retentates were dominated by aromatic rings and phenolic hydroxyls with high O/Cwa (weighted average of O/C) and low H/Cwa. Conversely, such dialysates had numerous aliphatic chains with high H/Cwa and low O/Cwa compared to SRFA. In particular, LMW-DOM below 200 Da was identified by Orbitrap MS. This work provides an operational program for identifying LMW-DOM based on the SRFA standard and MS analysis.