Friction stir welding of 1016 pure aluminum and T2 pure copper with 2 mm thickness was carried out in the form of lap welding of copper on the upper side and aluminum on the lower side. The growth of interface microstructure between 1016 pure aluminum and T2 pure copper welded by friction stir welding was studied. The growth mechanism of the intermetallic compound (IMC) layer in the Cu-Al lap joint was revealed by annealing at 300, 350, 400 °C. The intermetallic compound (IMC) layer in the lap joint grows again during annealing, and only the original structure of the intermetallic compound (IMC) layer grows at lower annealing temperature and holding time. At higher annealing temperature and holding time, the original structure of intermetallic compound (IMC) layer no longer grows, and a new layered structure appears in the middle of the original structure. There is a gradient change of microhardness in the nugget zone. With different holding times, different softening phenomena appear in the metals on both sides of copper and aluminum. When the hardness decreases to a certain extent, it will not continue to decrease with the increase of holding time. When the annealing temperature is 350 °C and 400 °C, the strength of the tensile sample increases first and then decreases with the increase of holding time. At the interface of Cu-Al, the fracture runs through the whole intermetallic compound (IMC) layer.