Humic acid (HA) is a supermolecule consisting of a variety of components, has a significant influence on the geochemical behaviors of Cr(VI), and is commonly examined as a single molecular unit without discriminating the relative role of each component. In this study, HA was separated into five fractions (> 100 KD, 30-100 KD, 10-30 KD, 3-10 KD, and < 3 KD) with ultrafiltration according to its molecular weight (MW). Fourier transform infrared spectroscopy (FTIR), solid-state 13C nuclear magnetic resonance (13C NMR), and Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) were used to examine the molecular characteristics of each component, and the link between the molecular composition and the adsorption of each component by goethite together with its effect on the adsorption of Cr(VI) were determined. The adsorption kinetics of the unfractionated HA by goethite showed an initial rapid stage with a subsequent slow process, and was well described by a pseudo-second-order model. Due to the small size, the adsorption of the < 3 KD fraction proceeded most rapidly among the five fractions, but attained the lowest equilibrium adsorption amounts. Based on the 13C NMR analysis, this result could be attributed to the contrasting difference in the content of aromatic carbon among the fractions (e.g.: 57.65% for > 100 KD and 21.89% for < 3 KD) since aromatic moieties were considered to be the primary contribution to the adsorption of HA. The FT-ICR MS analysis further showed that the 10–30 KD fraction contained 31.7% condensed polycyclic aromatic components and 25.8% aliphatic components (~ 2.5 times higher than the < 3 KD fraction; 10.6%), likely causing the inhibitory effect of the 10–30 KD fraction on the adsorption of Cr(VI), and its affect was higher than that of the < 3 KD fraction. Overall, this study provides insightful knowledge on the role of HA in regulating the partitioning of Cr(VI) between aqueous and solid phases at the molecular level.