By adjusting the rotation speed of separated pin and assisted shoulder, dual-rotation friction stir welding can reduce the softened region and improve the properties of joint. In this study, a tool system for dual-rotation friction stir welding was designed. Five-millimeter-thick 6061-T6 aluminum alloy was welded using the self-designed tool system. The effects of rotation speed of assisted shoulder on microstructure and mechanical properties of joints were analyzed. Defect-free joints were obtained under the process parameters used. Fine equiaxed recrystallized grains were found in both weld nugget zone and shoulder affected zone, while the grain size in shoulder affected zone appeared to be much smaller. The microhardness showed a noticeable decline in the weld zone, and the lowest value was located in heat-affected zone. Tensile test results demonstrated that all welded joints fractured at the interface of thermo-mechanically affected zone and heat-affected zone with ductile fracture mode.