Lipase from Y. lipolytica was successfully purified with aqueous two-phase system. Lipase from Y. lipolytica was concentrated in the salty phase, easier to extract. Aqueous two-phase system (ATPS) method was superior to traditional methods. Lipase purified with ATPS showed good thermostability until 50 °C. Purified lipase extract showed good stability at a wide pH range.