In this work, a new magnetic 3D graphene aerogel/CaCO3 nanocomposite was synthesized successfully using a one-step in situ self-assembly of graphene oxide in the presence of CaCO3 and Fe3O4 nanoparticles. The product was characterized using various techniques such as Field Emission scanning electron microscope (FESEM), Fourier transform infrared (FTIR), energy dispersive X-ray (EDX), vibrating sample magnetometer (VSM) and X-ray diffraction (XRD). The prepared nanocomposite was used as a novel absorbent to remove Acid Red 88 (AR88) dye from aqueous solutions as an anionic azo dye model. The effects of operational parameters such as absorbent dosage, dye concentration, pH and contact time on AR88 removal were investigated by using response surface methodology (RSM). From RSM results, the optimized values in the range of quantities used in this work for 100% removal of AR88 dye were found to be 87mg nanocomposite, 14mg/L dye (AR88) concentration, pH 6 and contact time 18min. Absorption of AR88 obeyed intra-particle diffusion kinetic model. These results suggest that the magnetic 3D graphene aerogel/CaCO3 nanocomposite is a good candidate for the rapid removal of AR88 from aqueous solutions.