In rivers, the distribution and reactivity of heavy metals (HMs) are affected by their binding affinity with sediment dissolved organic matter (DOM) and particulate organic matter (POM). The HM-OM binding affinity affected by the interaction between DOM and POM is not well studied. This study investigated the Ni binding affinity to size-fractioned overlaying water DOM and alkaline extracted sediment POM solution (AEOM). The DOM/AEOM filtrates (<0.45 μm) were sequentially separated into five nominal molecular weight (MW) solutions. The AEOM optical indicators had lower autochthonous, higher terrestrial sources, and lower aromaticity than the DOM. The Ni mass (72.3 ± 6.4%) was primarily distributed in the low molecular weight DOM (<1 kDa), whereas the Ni (93.5 ± 0.4%) and organic carbon (OC) mass (85.3 ± 1.0%) were predominantly distributed in the high molecular weight AEOM. The Ni and DOM binding affinity, ([Ni]/[DOC])DOM ratio ranging from 0.76 to 27.32 μmol/g-C, was significantly higher than the ([Ni]/[DOC])AEOM ratios, which ranged from 0.64 to 2.64 μmol/g-C. The ([Ni]/[DOC])AEOM ratio correlated significantly with the selected optical indicators (r = 0.87–0.92, p < 0.001), but the ([Ni]/[DOC])DOM ratio correlated weakly with the optical indicators (r = 0.13–0.40, p > 0.05). In the present study, the Ni binding affinity with size-fractioned DOM/AEOM agrees with the hypothesis of the DOM and POM exchange conceptual model in sediment. The POM underwent a hydrolysis/oxidation process; hence, AEOM had a high molecular weight and stable chemical composition and structure. The Ni mainly attached to the high molecular weight AEOM and the ([Ni]/[DOC])AEOM ratios had a strong correlation with the AEOM optical indicators. In contrast, DOM had a high ([Ni]/[DOC])DOM ratio in low molecular weight DOM.