Depositions of AA6061 aluminum alloy with different thicknesses (0.5, 1.0 and 1.5 mm) and homogeneous microstructure were successfully obtained through additive friction stir deposition (AFSD) technique. A self-developed in-situ process monitoring kit has been utilized to in-situ monitor the real-time temperature, force and torque during the AFSD process. Effect of thickness on the microstructure and mechanical properties are investigated based on the monitored parameters. With the electron back scattered diffraction (EBSD) analysis on a large area (4 × 4 mm), the synergism of dynamic recrystallization (DRX) and shear deformation is found to affect the microstructure. DRX is the main reason for the grains refinement which are remarkably reduced to 7 μm as the thickness increases. Whereas, the shear deformation exhibits a stronger effect on the texture. The texture intensity reduces and then increases as the thickness increases from 0.5 to 1.5 mm. Values of micro-hardness (46.8 HV), yield strength (106.0 MPa) and ultimate tensile strength (171.2 MPa) of the deposition are the highest when the thickness is the largest (1.5 mm) attributed to the lowest thermal cycle and evolution of DRX. All the findings provide useful guidance for the visualization and understanding of AFSD process.