In this work, based on excitation-emission matrix spectroscopy combined with parallel factor analysis (EEM-FARAFAC) and two-dimensional correlation analysis of synchronous fluorescence spectroscopy, Fourier transform infrared spectroscopy, and combination of two spectra (2D-SF-COS, 2D-FTIR-COS, and Hetero-2D-COS), the characteristics and metal-binding behaviors of DOM in Dongping Lake were explored for molecular weight (MW), fluorescence components, and functional groups. The results showed that the entire lake was governed by protein-like materials with low MW(< 1 kDa). The complexation occurred preferentially in protein-like materials for bulk DOM after adding copper (Cu2+) and lead (Pb2+), which were changed by fractionation for MW. The active points were aliphatic C-OH for DOM-Cu and phenol -OH or polysaccharide for DOM-Pb from 2D-FTIR-COS. The protein-like components possessed higher LogK than humic-like component during binding to Cu2+ or Pb2+. Moreover, the complexing affinities of DOM-Cu (LogKCu: 3.26 ± 0.87–4.04 ± 0.49) were higher than those of DOM-Pb (LogKPb: 2.66 ± 0.52–3.78 ± 0.36). On a spatial scale, high LogKCu and LogKPb were found in the center and entrance of the lake, respectively. Humic-like component C2 in the LMW fraction possessed a stronger binding capacity with Cu2+. This study affords new insights into the migration and conversion of HMs in lakes.