2060-T8 Al-Li alloy was friction stir butt welded under natural and water cooling conditions. Microstructures and mechanical properties of the welding joints were mainly compared and discussed. By spraying water on the top surface of stir zone, the grain size was reduced, attributing to the improvement of microhardness. The maximum tensile strength under the water cooling reached 461.1 MPa. The joint fractured at the stir zone due to the thickness reduction and the joint softening. The fracture surface consisted of many dimples with various sizes, indicating the typical ductile fracture. The strategy to apply the low heat input at the welding stage and high cooling rate at the cooling stage during FSW is necessary to obtain a high-quality FSW joint.