Hydrolysis lignin was treated with sub- and supercritical water (523–723 K and 10 MPa). As a result, depolymerization of lignin to mono- and oligolignols occurs. SEC data show water-soluble particles up to 4 nm after treatment of lignin by subcritical water (523 K and 10 MPa). After further treatment with supercritical water (723 K and 10 MPa), the concentration of water-soluble particles decreases by 2–3 times; and their size increased up to 10 nm. Molecular dynamics simulation of a model lignin particle in aqueous medium under standard (298 K, ρ = 0.997 g/cm3) and supercritical (673 K, ρ = 0.133 g/cm3) conditions was performed. Based on modeling, lignol monomers surrounded by solvate shells and water-soluble particles of lignin oligomers with a gel-like structure were identified as the structural units of the solutions. Under supercritical conditions, it causes the different ways of transformation of the system: further destruction of individual lignol molecules or condensation of lignols with the formation of insoluble precipitate.