This study investigates the effect of Zn interlayer thickness on the microstructure and mechanical properties of a dissimilar joint between an aluminum alloy (AA6061) and a magnesium alloy (AZ91), produced using friction stir welding (FSW). The presence of the Zn interlayer contributed to a more favorable distribution of intermetallic compounds (IMCs) in the stir zone (SZ). The Zn layer promoted the formation of Mg-Zn IMCs, which were discontinuously distributed, replacing the more continuous Al-Mg IMCs typically observed in dissimilar FSW joints. This discontinuous distribution is beneficial because it can mitigate brittleness and improve the overall mechanical properties of the joint. As a result of the optimized microstructure, the joint achieved a maximum tensile strength of 181 MPa with the 0.25 mm Zn interlayer, indicating enhanced mechanical performance. This demonstrates that careful selection of the interlayer thickness can play a critical role in controlling the microstructure and mechanical characteristics of dissimilar FSW joints.