Effective management and beneficial utilization of liquid digestate is becoming a bottleneck of anaerobic digestion. Electrodialysis exhibits considerable potential in liquid digestate valorization; however, the process is typically challenged by severe membrane fouling due to high organic matter content. In the present study, a bench-scale electrodialysis was carried out to treat fresh and mature digestate with an aim of investigating the behavior of dissolved organic matter (DOM) during electrodialysis using ultrahigh-resolution mass spectrometry. Organics that were easily transported across the ion-exchange membrane (IEM) had relatively high O/C ratios (0.208−0.414) contributed from carboxyls, as well as relatively low H/C ratios (1.15−1.55) and high aromatic indexes (0.257−0.504) contributed from the benzene rings. Chemical cleaning with HCl and NaOH exhibited a cleaning effect on 66%−69% richness of DOM and completely removed 33%−38% richness of foulants via deprotonation or protonation effects, whereas 36%−45% richness of DOM, which had significantly higher aromatic indices, could not be completely removed by chemical cleaning due to their high hydrophobic affinity for the polymer matrix of IEM. The speculated fouling mechanisms included electrostatic interactions, hydrophobic interactions, hydrogen bonding, and geometrical exclusion. The results of the present study could enhance our understanding of DOM behavior during electrodialysis at the molecular level and, in turn, provide insights into the mitigation and prevention of membrane fouling in electrodialysis for the treatment of other organic-rich wastewaters.