The objective of this work is to analyse the effect of variations in IMC thickness and microstructure at interface on the mechanical properties, for the RFW joints of Al6061 and mild steel. Rotary friction welding is a solid-state joining process which is advantageous towards joining of dissimilar materials. The rotary friction welding of Al6061 and mild steel is performed at combinations of two rotational speeds (1200 rpm and 1400 rpm) and three feed rates (10 mm/min, 20 mm/min and 30 mm/min). The microstructural characterization, tensile and hardness testing of the joints is performed. A concave joint interface is noticed due to inhomogeneous plastic deformation along the radial direction from center to workpiece periphery. Similarly, inhomogeneous intermetallic compounds formation along the radial direction at the joint interface is observed, with higher intermetallic compound thickness near the workpiece periphery. The grain refinement on Al6061 side of the interface is attributed to the continuous dynamic recrystallization. Dynamic recovery is noticed at the mild steel side. The crack initiates at the IMC rich region near the periphery and follows the IMCs to grow radially inwards. Along the radial direction from periphery to the center, the reduction in IMC thickness and increase in DRX region thickness resists the growth of the crack. Brittle failure is observed in the IMC rich regions near the periphery and ductile failure is noticed near the center. An increase in IMC thickness reduces the joint strength and wider DRX region improves the joint strength. This combination led to the maximum tensile strength for the joints prepared with intermediate feed rate of 20 mm/min. A maximum joint tensile strength of 136 MPa is achieved, which corresponds to 65 % joint efficiency.