The relationship between thermal cycle, microstructures and properties of the joint in bobbin tool friction stir welding (BT-FSW) of aluminum alloys thick plates has not been reported in the literature, and the variations of microstructures and properties along the thickness direction needs to be explored. The objective of this paper is to interpret the evolution of thermal cycle, microstructures and mechanical properties of 16 mm thick 6061-T6 aluminum alloy BT-FSW joint in the thickness direction. With a traverse speed of 200 mm/min and 300 r/min of rotation speed, the thermal cycle temperature of the joint central layer is about 6 degrees C lower than that of the Shoulder Affected Zone (SAZ), and the Retreating Side (RS) are about 20 degrees C higher than the Advancing Side (AS). In order to illustrate the differences in the thickness direction of the joint, the joint was divided equally into three slices along the thickness direction. It is found that the equiaxed grains sizes of the Stir Zone (SZ) are 19.6 mu m, 15.2 mu m and 21.3 mu m respectively in each region of the SZ1, SZ2 and SZ3 in the thickness direction, and the recrystallization extent of the SZ1 and SZ3 is higher than that of the SZ2. Transition from the SZ to the Heat-Affected Zone (HAZ), where the precipitates changes from the cluster-GP zone and beta phase to the beta" and beta' phases. The Vickers hardness curves for the cross-section of the joint are W-shaped, and the minimum Vickers hardness is found in the transition zone of the Thermal-Mechanically Affected Zone (TMAZ) and HAZ, which is 60 HV, and the SAZ has roughly 10 HV greater hardness than that of the central layer of the SZ. Along the thickness direction, the average tensile strength of the slices #1, #2 and #3 of the joints are 188 MPa, and 160 MPa, and 180 MPa respectively. The fracture of the three slices is ductile fractures.