The microstructure, mechanical property and corrosion behavior of 6061 Al/AZ31 Mg friction stir welding lap joints with Zr interlayer at different rotation rates were investigated. The results show that the Zr interlayer suppresses the defects of flashes and tunnels. The welding materials are joined via the mechanical interlocking in the stir zone (SZ) and the intermetallic compounds are formed at the overlapping interface. The degree of thermoplastic flow and mechanical interlocking in the SZ increase with increasing rotation rate, which form smaller Zr fragments and thinner strips. The transitional widths of the thermal-mechanical affected zone (TMAZ)/SZ interface as well as the overlapping interface tend to increase as the rotation rate increases. The hardness distribution on the cross-sections of joints along advancing side and retreating side are asymmetric, which has higher hardness near the welding centerline. The tensile shear load of Al/Zr/Mg joints firstly increases and then decreases with increasing rotation rate and the fracture position is located at the TMAZ/SZ interface. The joints exhibit a differential corrosion behavior in the 3.5% NaCl solution. The Al alloy is uniformly corroded, the Mg alloy is locally pitting corroded and the Zr interlayer is not corroded. The corrosion resistance of joints is deteriorated in some degree with increasing rotation rate.