Friction stir welding is a solid state process in which no fusion occurring on it. This method of welding is uses for metals that have low weldability or their fusion welds haven’t good quality. The effect of friction stir welding parameters, including rotational speed, linear speed, shoulder diameter and pin diameter on AA5052 to AA6061 dissimilar joints was studied in this paper. These parameters were optimized Using Taguchi method of Design of Experiments. then thermal simulation of process was done with ABAQUS software in which the temperature distribution results were in good agreement with the simulation results. The results of specimens tensile tests were confirmed by metallography and micro-hardness tests result. With increasing the linear speed and reducing the rotational speed, heat input reduced and grain size of all weld areas is decreased. The retreating side of all instances had a smaller grain size than advancing side. This is because of the thermal properties of 6061 alloy (higher conductivity and lower heat capacity), which leads to lower peak temperature and higher thermal diffusivity on that. The optimal parameters including rotational speed of 1400 rpm, linear speed of 80 mm/min, shoulder diameter of 15 mm and a pin diameter of 3.5 mm, was achieved. The maximum tensile strength of 228.3 Mpa achieved in rotation speed of 1400 RPM, linear speed of 80 mm/min, shoulder diameter of 15 mm and pin diameter of 3.5 mm.