In this work, molecular dynamics simulation (MD) was used for studying the liquid-liquid extraction of acetic acid and acetone from water in the presence of nanoparticles. In the next step, the solubility parameter of acetic acid and acetone were predicted at 1 atm and different temperatures along with the solubility parameter of solvents and water at 25 °C and 1 atm. Three pure systems and three systems with different concentration of nanoparticles were investigated to show the effect of cell size or number of molecules on the solubility parameter. With the addition of SiO2 nanoparticles to the solvents, at low concentrations of nanoparticles (0.01–0.1 vol%), the solubility parameter is increased due to the Brownian motion. With the further increase concentration of the nanoparticles, the solubility parameter decreases due to the accumulation of nanoparticles. The difference between the solubility parameter of benzene and acetone was 0.414 (J/cm3)0.5 and 3.13 (J/cm3)0.5, with and without the presence of SiO2 nanoparticles, respectively. Finally, toluene was found to be the best solvent for acetone and acetic acid at silica nanoparticles concentration of 0.062 vol%.