Heavy metals are not degraded in aquatic environment and the transportation of heavy metals greatly affects their bioavailability. Dissolved organic matter (DOM) plays an important role in the transportation of heavy metals in aquatic environment. Previous research has proven that molecular size and composition of DOM can be changed under the action of microbial degradation and self-assembly. How these changes of DOM affect the transportation of heavy metals is unknown. We collected the colloidal precursors (i.e. <1kDa) and bulk DOM from Haihe river and incubated them in the dark for 21 days. Ultrafiltration, fluorescence spectroscopy and parallel factor analysis (PARAFAC) were used to divide DOM into different molecular size and examine the change of DOM in molecular size and composition during the incubation. Inductively coupled plasma mass spectrometry (ICP-MS) was to examine the transportation of heavy metals between different molecular size. Results shows that the concentrations of total organic carbon, carbohydrates, and protein-like substances decreased while the concentration of humic-and fulvic-like substance remained relatively constant during incubation. Under the action of microbial degradation and self-assembly, the dissolved organic matter in <1kDa and 10kDa to 0.45μm molecular size was reduced while the dissolved organic matter in 1kDa to 10kDa and >0.45μm section was increased, which suggested a transportation pathway of DOM. The carbohydrates and protein-like substances decreased especially in >10kDa section suggested that the carbohydrates and protein-like substance are easily degraded by microorganisms. The concentration of humic-and fulvic-like substance remained relatively constant during incubation but in molecular size level they showed a transformation pathway from the <1kDa to colloids (1kDa–0.45μm) and further to microparticles (>0.45μm). Meanwhile, different heavy metals had different transportation. Fe showed the highest affinity with dissolved organic matter of 1kDa to 10kDa, and mainly transported among high molecular size DOM. Zn and Cr showed the intermediate affinity with the dissolved organic matter of 1kDa to 10kDa and mainly transported between 1kDa to 10kDa and <1kDa section. Cd showed the lowest affinity with dissolved organic matter and mainly exist in <1kDa section. This finding provides new insights into the transportation of heavy metals in aquatic system.