In this study, a highly efficient and eco-friendly porous cellulose-based aerogel was synthesized by grafting polyethyleneimine onto quaternized cellulose (PQC) to remove the anionic dye Congo Red (CR). The prepared aerogel had a good flexibility and formability. The adsorbents were characterized by scanning electron microscopy (SEM), Fourier transform infrared (FTIR) spectroscopy and elemental analysis. The results showed that there were many amino groups on CE/PQC aerogel and the structure was porous, which increased the adsorption capacity. The effects of initial concentration, adsorbent dose, contact time, temperature, and pH on the dye sorption were all investigated. The adsorption mechanism was also explored, including adsorption kinetics, adsorption isotherms and thermodynamic studies of adsorption. The results showed that the adsorption kinetics and isotherms fitted the pseudo-second-order kinetic model and Langmuir isotherm, respectively. The Langmuir isotherm revealed that the maximum theoretical adsorption capacity of the aerogels for CR was 518.403 mg g−1. The thermodynamic parameters including Gibbs free energy change (ΔG0), enthalpy change (ΔH0) and entropy change (ΔS0), showed the adsorption process was exothermic and spontaneous. These results imply that this new absorbent can be universally and effectively used for the removal of dyes from industrial textile wastewater.