The accelerated rate of industrial growth causes a lot of pollutants to be released into the environment. Therefore, the present work aimed at synthesizing a novel and environmentally friendly nanocomposite for eliminating dyes from wastewater. The (silica-alumina13 %)-Cu2+/polyaniline ((Si–Al)–Cu2+/PANI) nanocomposite was synthesized by the oxidative polymerization of aniline in the presence of (Si–Al)–Cu2+ composite. The nanocomposite was characterized by the FT-IR, XRD, BET, SEM, TEM, and EDX techniques. Its surface area was 287.7 m2/g and the pore diameter was 1.92 nm. The pseudo-second-order kinetic and the Langmuir isotherm models offered a satisfactory fit to the adsorption data. The removal percentage of the Acid blue 25 dye (AB25) by the nanocomposite reached 99 % within 60 min at pH 2, while the removal capacity was 135.86 mg/g. Based on the adsorption-desorption cycle results, the efficiency of the nanocomposite (99.7 %) remained unchanged up to the third cycle with a small decrease afterward. To corroborate the experimental results, a molecular modeling study was carried out using the basis function 6–311++G(d,p) and the DFT method to obtain the best molecular structure, physicochemical properties, and spectroscopic spectra of AB25 in the gas phase and water solvent. The electrostatic potential, Fuki functions, natural bond orbital, time-dependent DFT, and theoretical FT-IR were calculated. Furthermore, the adsorption of AB25 on the nanocomposite surface was verified by the Monte Carlo simulations. The computed data correlated well with the experimental results.