Al-Li alloys are widely applied in aircraft structures owing to their unique properties, such as low density, high strength and stiffness, outstanding low temperature performance, corrosion resistance and superplasticity. 2099-T83 and 2060-T8 are two new Al-Li alloys which have great potential to fabricate the fuselage panels of aircraft. The application of traditional fusion welding on joining Al-Li alloys is limited by cavity, high thermal stress, high thermal strain and low joint strength produced during melting and solidification. Friction stir welding (FSW) is an innovative solid-state joining technology. Compared with traditional fusion welding, FSW is capable of achieving high-quality welded joint in similar or dissimilar high-strength aluminum alloys due to its excellent performance, such as low energy consumption, low stress and strain, fewer metallurgical defects and distortion under reasonable processing parameters. Weld nugget zone (WNZ), thermo-mechanically affected zone (TMAZ) and external heat affected zone (HAZ) will be produced in the FSW joint. The micromorphologies and bonding interface among WNZ, TMAZ and HAZ have a significant effect on mechanical properties of welding joint. In this work, lap joints of 2099-T83 and 2060-T8 Al-Li alloy with 2 mm thickness were achieved by FSW. The interface microstructure of joints obtained by employing different tool rotation speeds and pin lengths was characterized by OM and SEM. The results showed that the obvious bonding interface was observed in the weld zone, and the bonding interface changed from smooth to zigzag with the rotation speed raising from 600 r/min to 800 r/min and pin length decreasing from 3.0 mm to 2.5 mm. In addition, micro-hardness of the weld zone was lower than the parent metal, and the lowest micro-hardness appeared in the transition region between the thermo mechanically affected zone and the weld zone (WZ) and the results of peel tests showed that the average failure load of joint with serrated bonding interface was up to 654 N. The failure occurred in the transition zone between the TMAZ and WZ of the 2060-T8 side, and the toughness-brittleness fracture mode appeared. Furthermore, the microhardness of the weld zone improved, while the failure load of the FSW joint with serrated bonding interface decreased 20% under artificial aging treatment with the temperature of 150 ℃ and the holding time of 20 h. The brittleness fracture mode existed in this condition. The pin length had a great effect on the morphology of bonding interface and mechanical property of welded joint.