In recent decades, the concentration of dissolved organic matter (DOM) in aquatic ecosystems has gradually increased, leading to water pollution problems. Understanding the interfacial chemical processes of DOM on natural minerals is important to the exploration of high-efficiency absorbents. However, studying DOM chemical processes and adsorption mechanisms are still challenging due to the complex DOM structure and environmental system. Hence, we characterized the microstructure changes after the formation of amorphous calcium phosphate (ACP) at the interface of montmorillonite (Mt) minerals in a simulated environment system. Combined with atomic force microscopy and density functional theory (DFT) simulation, the mechanism of interfacial interaction between Mt-ACP and DOM was characterized at the molecular level. Moreover, we further evaluated the adsorption behavior of Mt-ACP as a potential adsorbent for organic matter. The comprehensive investigation of humic acid adsorption, intermolecular force, and DFT simulation is conducive to our understanding of the interfacial interaction mechanism between organic matter and noncrystalline minerals in aquatic environments and provides new perspectives on the application of clay-based mineral materials in pollutant removal under exposure from DOM.