In this study, the pinless friction stir spot welding of aluminum–copper composite with Zn interlayer was analyzed under experimental measurement and finite element method. The role of shoulder diameter, 16, 18, and 20 mm, and the number of spot pass, one to three pass, on microstructure, mechanical properties, and thermal history of weld samples were investigated. Based on the obtained results, there is a good agreement between numerical data and experimental analyses. It was shown that the heat source, due to plastic deformation and friction, increased as the shoulder diameter was increased, whereas the stress distribution in the weld samples was reduced. In addition, the thickness of the Zn interlayer at the joint interface changes when shoulder size increases from 16 to 20 mm, due to high temperature and intermixing between materials. From the microstructure analysis, the grain size in the joint zone gradually decreases as the spot pass increases from 1 to 3. It was concluded that the shoulder diameter of 16 mm with three spot passes showed the best result of 7.45 kN. Depending on X-ray diffraction analyses of the fracture surfaces, three primarily intermetallic phases including the Al2Cu, CuZn5, and CuZn2 were determined in the weld interfaces. Based on finite element method analysis, the axial compressive stresses showed the lowest profile as the shoulder diameter of the tool is 16 mm. Finally, the ductile fracture was detected as the main fracture mechanism for the joint sample with optimal joining conditions.