This study investigated the distribution of copper in sediment dissolved and particulate organic matter (DOM and POM) based on their size. The DOM and alkaline extracted POM (AEOM) were separated into five size fractions using a cross-flow ultrafiltration (CFUF) system. The results showed that Cu mass was mainly distributed in the low molecular weight (<1 kDa, LMW) fraction of the DOM with an average range of 78.1–83.1%. Conversely, the high molecular weight (1 kDa–0.45 μm, HMW) AEOM fraction had a higher distribution of Cu mass with an average range of 92.6–93.3%. The Cu and AEOM binding affinity ratios (CuBAAEOM) ranged from 17.0 to 149.6 μmol/g-C in site-1 and from 20.6 to 143.7 μmol/g-C in site-2. The HMW CuBAAEOM ratios were significantly higher than the LMW ratios. The Cu and DOM binding affinity ratios (CuBADOM) ranged from 5.6 to 358.6 μmol/g-C and 17.2 to 126.6 μmol/g-C in site-1 and site-2, respectively. However, the LMW CuBADOM ratios were significantly higher than the HMW ratios. Optical indices suggested that the AEOM had more aromaticity and terrestrial and allochthonous contributions than the DOM. The optical indices were significantly correlated with the CuBAAEOM ratios but weakly correlated with the CuBADOM ratios. Sediment exchange between POM and DOM may affect copper distribution. DOM has a low-molecular-weight composition, while POM retains high-molecular-weight organic matter.