The 6061 aluminum alloy and QP980 steel were lap-welded by friction stir welding (FSW) technique, and the effect of different probe lengths of 1.5 and 2.1 mm on the microstructures and properties of welded joints was investigated. Results show that the FSW lap-welded joints of 6061 aluminum alloy/QP980 steel consist of three layers: the upper layer is aluminum alloy, the middle layer is composed of Fe, Al, and intermetallic compounds, and the under layer is steel. When the probe length is 2.1 mm, the aluminum layer contains scattered steel fragments. Two kinds of intermetallic compounds can be detected: the dark gray layer close to Al is Fe₄Al₁₃ phase, and the one close to steel is Fe₂Al₅ phase. With extending the probe length, the fracture load of the joints is decreased from 4 kN to 3 kN. The joints welded by short probe fracture at the bonding interface, whereas those welded by long probe fracture at the mixture zone of Al and steel. The fracture position change is caused by the porosities and steel fragments. In addition, the steel fragments embedded in the Al matrix promote the stress concentration and crack initiation during the deformation process, therefore decreasing the mechanical properties of the joints.