The association of soil organic matter (SOM) with iron (Fe) oxyhydroxides, particularly ferrihydrite, plays a pivotal role in the biogeochemical cycling of carbon (C) in both terrestrial and aquatic environment. The aging of ferrihydrite to more crystalline phases can impact the stability of associated organic C, a process potentially influenced by aluminum (Al) substitution due to its abundance. However, the molecular mechanisms governing the temporal and spatial distribution of SOM during the aging process of Al-substituted Fe oxyhydroxides remain unclear. This study aims to bridge this knowledge gap through a comprehensive approach, utilizing batch experiments, solid characterization techniques, and atomic force microscopy (AFM) based peak-force quantitative nanomechanical mapping (PF-QNM). Batch experiments revealed that humic acid (HA) was released into the aqueous phase during aging, with Al inhibiting this release. Various solid characterization methods collectively suggested that Al hindered the crystalline transformation of ferrihydrite and significantly preserved HA on the surface of newly formed hematite, rather than it being occluded within the interior of the new minerals. Results from 3-Dimensional fluorescence spectroscopy (3D-EEM) and Fourier-transform infrared spectroscopy (FTIR) indicated that the structure of HA remained constant, with the carboxyl-rich and hydroxyl-rich portions of HA fixed at the mineral interface during the aging period. Furthermore, we developed AFM-based PF-QNM to both quantify and visualize the interactions between Fe oxyhydroxides and HA, demonstrating variations in HA affinity among different Fe oxyhydroxides and highlighting the influence of the Al substitution rate.