Heat input (HI) is the major factor that affects the surface quality, microstructure and mechanical properties of the deposition during the additive friction stir deposition (AFSD) process. Effect of HI on the microstructure and mechanical performance of the AFSDed AA6061 has been in-depth explored via adjusting the values of traverse speed (v) and layer thickness (t). Results indicate that deposition with a higher HI promotes the material flow behavior as well as the plastic deformation, which effectively enhances the grain refinement and structural uniformity, and avoids the formation of defects. Meanwhile, TEM results confirm that the enhanced HI leads to the formation of a higher volume fraction of the finer precipitations (MgSi and AlFeSi phases), which assists in suppressing abnormal grain growth phenomenon and improves the bonding strength of the deposition. As HI decreases, the transfer efficiency of materials clearly reduces because of the incompletely softened materials, causing less plastic deformation and poor interlayer bonding strength of the deposition. The deposition with the lowest HI displays the worst tensile properties with the lowest micro-hardness (107 HV), YS (273 MPa) and UTS (303 MPa).