Dissimilar butt joint of pure aluminum and commercially pure copper was prepared using friction stir welding (FSW) process and subsequent post-weld heat treatment (PWHT) was also performed to improve the mechanical properties of the joints. The microstructural evolution of the intermetallic compounds (IMCs) was principally characterized by optical microscopy (OM), scanning electron microscopy equipped with energy diffraction spectrometer (SEM-EDS), X-ray diffraction (XRD), electron backscatter diffraction (EBSD) and high-resolution transmission electron microscopy (HRTEM). The results suggested that the IMCs layer played a critical role on the metallurgical bounding. A 1.9 μm thickness of AlCu IMCs layer successfully achieved by the post annealing treatment which was composed of dominated Al2Cu phase with average grain size of 0.72 μm and small proportion of Al4Cu9 phase. This thin IMCs layer with very fine grain structure and further refined Al matrix in stir zone promoted the improvement of total joint strength from 79% towards 95% of Al base material. Moreover, the failure mode of the FS Welds converted into the mixed fracture from original brittle fracture. While the very low strength with high brittleness of the joint was mainly attributed to the thicker thickness of IMCs layer containing coarse Al2Cu grains with average grain size of 2.6 μm, which produced by the solution treatment. It was established that the existence of the IMCs layer was the main contribution to the distinct rise in microhardness. In addition, the high fraction of high angle grain boundaries of Al2Cu phase indicated the occurrence of grain bulging mechanism through grain boundary migration during annealing treatment. The grain growth behavior of IMCs layer revealed that a core-shell structured AlCu-Al4Cu9 particles probably occurred in the Al2Cu matrix.