Microstructural characterization and temperature analysis have been performed in friction stir welding (FSW) of A383 and 5052 dissimilar aluminum alloys. Marked difference in microstructure was observed between joints with different arrangements of materials. The temperature at four points on each side of the joint line was measured during FSW in various conditions. In addition, an analytical model assumed that the work generated by the rotation of the tool led to the work for stirring materials and heat generation of the material and the tool. The temperature of the retreating side (RS) for the joint of the advancing side (AS):A383/RS:5052 was about 50K higher than that of AS, while the temperatures of AS and RS for the joint of AS:5052/RS:A383 were almost the same. The experimental temperature could be calculated reasonably by using the model with assumption of the work for stirring the material.