The synthesis of new environmentally friendly and biocompatible material is an exciting research field to remove various pollutants from water/wastewater samples. The main objective of this paper is the successful synthesis of an Eco-friendly and novel modified silica aerogel (NMSA) by adding a small amount of Quince seed mucilage (QSM, 0.05 wt%) to water glass precursor and an ambient pressure drying method. The prepared NMSA was characterized by Fourier transform infrared spectroscopy (FTIR), scanning electron microscope (SEM), and N2 adsorption/desorption isotherms. Results showed that adding a small amount of QSM to the precursor causes the formation of relatively uniform nanoparticles with an approximate size of 20 nm. The synthesized NMSA was then used for Pb(II) removal from an aqueous solution. Pb(II) adsorption in NMSA was about 30% more than raw Silica aerogel (SA). After performing some preliminary experiments and confirming the excellent efficiency of the NMSA in Pb(II) removal, RSM (response surface methodology) study via a central composite design (CCD) optimization approach was made to study the effects of the interaction of the influencing variables on the adsorption efficiency. The maximum Pb(II)-removal efficiency of 75% was achieved for the optimized run with conditions of pH: 4, contact time: 62 min, NMSA dosage: 1.4 g/L, and initial Pb(II) concentration: 50 mg/L. The Pb(II) removal by the modified NMSA adsorbent well obeyed the Langmuir isotherm and a pseudo-second-order rate kinetics model.