ABSTRACT The primary aim of this study is to enhance our understanding of friction stir welding (FSW) at the atomic level. To accomplish this, we utilised molecular dynamics simulations to examine the nanoscale fusion welding of dissimilar metals, i.e. aluminium and copper, through the FSW method. Our particular focus was on how the rotation speed of the tool affects structural changes and defect evolution during the nanoscale FSW process. Our research findings revealed that the region subjected to frictional stirring undergoes a phase change as a result of extensive plastic deformation during the FSW operation. Notably, stacking faults and similar defects were predominantly observed on the advancing side as the tool rotated and moved into the friction stir zone. Further, investigation of atomic shear strain snapshots indicated that higher rotational speeds resulted in a broader and more scattered friction stir zone, requiring a longer recovery time compared to slower rotational speeds. Additionally, the changes in atomic concentration during FSW have been studied using displacement vectors, concentration profiles and diffusion coefficient parameters. We also conducted simulation-based tensile and shear deformation tests, which revealed that higher tool rotational speeds led to enhanced material interlocking, consequently improving the mechanical strength of the FSW joints.