Soil organic matter (SOM) is heterogeneous and a complex mixture, whose concentration, chemical composition, and structure are strongly associated with the binding behavior of heavy metals (HMs) in soil. The HM-SOM binding affinity affects the HM biotoxicity and bioavailability in the environment. This study investigated Cu’s distribution and binding affinity on five size-fractioned alkaline-extracted soil organic matters (AEOMs) taken from paddy fields. The fractioned AEOMs were M-A (100 kDa −0.45 μm), M-B (3–100 kDa), M-C (1–3 kDa), M-D (0.3–1.0 kDa), and M-E (<0.3 kDa). The average organic carbon (OC) mass percentages were 10.0, 40.3, 6.3, 5.0, and 38.4%, and Cu mass percentages were 9.8, 66.7, 4.7, 4.7, and 14.1% for fractioned M-A, M-B, M-C, M-D, and M-E solutions, respectively. The Cu and AEOM binding affinity, [Cu]/[DOC] ratios, ranged from 3.1 to 127.6 μmol/g-C with 41-fold variation. The ratio order was 63.5 ± 32.3 (M-B) > 32.8 ± 12.8 (M-A) > 28.0 ± 10.5 (M-D) > 24.25 ± 10.7 (M-C) > 12.5 ± 6.0 (M-E) μmol g-C−1. Cu preferred binding with size-fractioned AEOMs ranging from 3 to 100 kDa. The specific ultraviolet absorbance at 254 nm (SUVA254), the fluorescence index (FI), and the biological index (BIX) were significantly correlated with the [Cu]/[DOC] ratios. In each site, the combined bulk and the five size-fractioned AEOMs, the selected optical indicators had a significant correlation with the corresponding [Cu]/[DOC] ratios. Cu-AEOM binding affinity was enhanced by AEOM rich in aromaticity. However, high microbial and autochthonous AEOM origins decreased the binding affinity.