In this research, mesoporous calcium aluminate nanostructures (meso-CaAl2O4) were synthesized using a citric acid-assisted sol–gel auto-combustion process as the potential adsorbent to eliminate toxic triphenylmethane dye malachite green (MG) from synthetic/real effluent. The surface morphology of meso-CaAl2O4 was highly porous with nanometric size and non-homogeneous surface. The specific surface area, total pore volume, and BJH pore diameter of meso-CaAl2O4 were 148.5 m2 g−1, 1.39 cm3 g−1, and 19 nm, respectively. The meso-CaAl2O4 also showed a very high heat resistance, due to losing only 7.95% of its weight up to 800 °C, which is mainly related to the moisture loss. The optimal adsorption conditions were obtained based on response surface methods (RSM)-central composite design (CCD) techniques. The Langmuir isotherm model was used for fitting the adsorption measurements, which presented 587.5 mg g–1 as the maximum adsorption capacity of the dye. The data obtained from the adsorption kinetics model were found to correspond to the pseudo-second-order model. Also, the thermodynamic parameters including enthalpy change (ΔH°), entropy change (ΔS°), and Gibbs free energy change (ΔG°) indicated that MG dye adsorption by the meso-CaAl2O4 was feasible, endothermic, and occurred spontaneously. Furthermore, the meso-CaAl2O4 was regenerated by microwave irradiation under 900 W at 6 min, and the MG dye removal efficiency was remained over 90% after the five cycles of microwave regeneration.