The invention discloses a treatment method and system of a water-based oil-containing solution. The treatment method comprises the following steps: mixing the water-based oil-containing solution with a water-soluble organic solvent so as to generate a mixture of solid precipitate and a liquid phase; separating the solid precipitate from the liquid phase; heating or cooling the liquid phase to the target temperature and separating the liquid phase into an organic phase and a water phase at least; and removing at least a part of oil substances out of the organic phase.