7075-T6 Al and AZ31B Mg dissimilar alloys were friction stir lap welded with or without a Zn filler, and the effect of heat input on the joint quality was systematically studied. The experimental and finite element simulation results displayed that the formation characteristics and microstructures of the joint with or without the Zn filler were significantly affected by the heat input. The tensile shear load of joint with or without the Zn filler increased first and then decreased with the decrease of the welding speed from 200 to 50 mm/min. Moreover, the peak temperature in the stir zone was significantly decreased by the Zn filler addition, and the high temperature zone narrowed along the plate thickness direction. These changes of heat input made that longer mixing region boundary length and larger effective lap width were attained as the Zn filler was used. In addition, due to the replacement of Al-Mg intermetallic compounds (IMCs) by Al-Mg-Zn and Mg-Zn IMCs which were less harmful to the joint, the tensile shear load of the joint with the Zn filler was obviously enhanced compared to that of the joint without the Zn filler at each welding speed. The maximum tensile shear load of 7.2 kN was obtained at the welding speed of 100 mm/min.