Friction stir additive manufacturing (FSAM) is an advanced solid-phase forming technology based on the principle of friction stir. As no heat source is required, the FSAM process can avoid metallurgical defects during melting and solidification of the material. The FSAM also conserves energy and protects the environment. To replace the traditional forming technology with a heat source, current research aims to optimize the forming process parameters of aluminum and magnesium alloys. Similarly to the friction stir welding process, increasing the temperature in the FSAM process will dissolve part of the strengthening phase, coarsening the particles and softening the welding core area. In addition, during layer-by-layer stacking in FSAM, the stir tool will re-stir the previously formed area, introducing a new thermal cycle during the stirring process. Because the changes in the temperature and stress field are more complex in the FSAM process than in the friction stir welding process, the influence of microstructure evolution on the mechanical properties of materials in the FSAM process is worthy of investigation. In this study, a multilayer defect-free FSAM material was fabricated from 2-mm-thick 6061 aluminum alloy sheets. The microstructural evolution along the building direction was observed during the FSAM process to investigate its effect on the microhardness and tensile properties. Dynamic crystallization formed fine equiaxed grains in the stir zone, which were further refined after re-stirring in the overlapping interface regions. The tensile strength and elongation of the FSAM material were 47.7%-55.2% and 144.6%-148.8% those of the base material, respectively. Multiple thermal cycling weakens the performance of the overlapping interface regions. The spherical α-Al(MnCrFe)Si phase plays a strengthening role in the matrix. Extensive dissolution of the strengthening phase during the FSAM process is mainly responsible for the performance deterioration of the FSAM material. After heat treatment at 520 ^oC for 1 h and at 165 ^oC for 18 h of aging, the properties of the FSAM material were largely improved: the hardness slightly increased from that of the base material and the tensile strength reached 87.2%-91.9% that of the base material.