Melanoidins are hazardous coloring and polluting polymers widely found in the effluents of molasses-based distilleries and are negatively charged owing to carboxyl groups included in their chemical structures. A CHTA-modified metal–organic framework/chitosan composite aerogel (CHTA-MOF/CAG) was fabricated to serve as a melanoidin scavenger. The introduced functional monomer with an electropositive charge provides an effective binding site for capturing melanoidins. CHTA-MOF/CAG features highly dispersed CHTA target functional monomers and three-dimensional porous structures, thus achieving a larger adsorption capacity and higher mass transfer efficiency. The equilibrium adsorption of CHTA-MOF/CAG for melanoidins was as high as 465 mg/g, and the melanoidin removal percentage was 92%. Interaction, kinetics, and mass transfer micromechanisms studies revealed that two layers of melanoidins adsorbed on the CHTA-MOF/CAG surface were mostly mediated by the electrovalent linkage between carboxylate and quaternary ammonium, followed by electron sharing. On average, one melanoidin molecule can be shared by three to four quaternary ammonium groups of CHTA-MOF/CAG, indicating a parallel adsorption orientation. Adsorption onto active sites is the rate-controlling mechanism of the system, and the diffusion of melanoidins to CHTA-MOF/CAG is fairly rapid. CHTA-MOF/CAG showed a higher affinity for lower molecular weight melanoidins than pigments with larger molecular sizes.