Dissolved organic matter (DOM) is ubiquitous in natural waters which exhibits obvious effects on the toxicity of heavy metals. However, information on the toxicity of heavy metals in the presence of DOMs with different molecular weights (MWs) was still unclear. In this study, Suwannee river humic acid (SRHA) and algae-derived organic matter (ADOM) were selected as typical terrestrial and microbial DOMs, with the bulk DOMs fractionating into high MW (HMW-, 1kDa ~ 0.45μm) and low MW (LMW-, < 1kDa) fractions to explore the MW-dependent heterogeneities in the bioaccumulation of Pb to Chlorella vulgaris. Results showed that, regardless of DOM types, the LMW fraction exhibited more acidic groups and humic-like substances than the HMW counterparts. Presence of bulk DOM can decrease the bioaccumulation of Pb, while the specific effects were MW- and type-dependent. The LMW-SRHA enhanced the bioaccumulation of Pb while the HMW counterpart alleviated the effects. However, both the HMW- and LMW-ADOM can reduce the bioaccumulation of Pb to C. vulgaris. Moreover, the correlation analysis showed a significant positive correlation between the content of phenolic-OH and the adsorbed/internalized amounts of Pb, demonstrating that the phenolic-OH played a critical role in altering the bioaccumulation of Pb. The results obtained in this study suggest that distribution of MWs, number of acidic functional groups, and metal complexation capacity within DOM pool should be considered for the eco-environmental risk assessment of heavy metals in aquatic environments.