Soil humic substances (SHS) are heterogeneous, complex mixtures, whose concentration, chemical composition, and structure affect the transport and distribution of heavy metals. This study investigated the distribution behavior of two heavy metals [cadmium (Cd) and nickel (Ni)] in high molecular weight SHS (HMHS, 1 kDa–0.45 μm) and low molecular weight SHS (LMHS, <1 kDa) extracted from agricultural soils. The HMHS mass fractions were 45.1 ± 19.3%, 17.1 ± 6.7%, and 57.7 ± 18.5% for dissolved organic carbon (DOC), Cd, and Ni, respectively. The metal binding affinity, unit organic carbon binding with heavy metal ratios ([Me]/[DOC]), were between 0.41 ± 0.09 μmol/g-C and 7.29 ± 2.27 μmol/g-C. Cd preferred binding with LMHS (p < 0.001), while Ni preferred binding with HMHS (p < 0.001). The optical indicators SUVA254, SR, and FI were 3.16 ± 1.62 L/mg-C/m, 0.54 ± 0.18 and 1.57 ± 0.15, respectively for HMHS and 2.65 ± 1.25 L/mg-C/m, 0.40 ± 0.17, and 1.68 ± 0.12, respectively for LMHS. The HMHS contained more aromatic and lower FI values than LMHS. Multilinear regression showed a significant positive correlation between the measured predicted [Me]/[DOC] ratios (r = 0.52–0.72, p < 0.001). The results show that the optical indices can distinguish the chemical composition and structure of different size SHS and predict the binding ability of Me-SHS.