The friction stir welding (FSW) is a newly developed solid-state welding technique, which addresses a number of practical issues such as reducing melt related defects by reducing welding temperature. This provides an opportunity for dissimilar metal welding and provides high quality joints. In the present study friction stir welding was performed on AA6063 and copper alloys by conventional FSW method and with the aid of external flame heating during the FSW process. The concept behind the experimentation is to perform the welding at low RPM to improve the material mixing and joint properties. The microstructure, phase constituents and mechanical properties of FSW joints were studied through optical metallography, SEM, X-ray diffraction, micro hardness, and tensile tests. Al2Cu and Al4Cu9 intermetallic were formed during the conventional and assisted flame heating FSW process which were distributed in the nugget zone. Due to the flame heating, copper and aluminum alloys get softer and leads to distribution of intermetallic as lamellar structure. The values of tensile strength for conventional friction stir welding, and assisted flame heating FSW are 69 MPa, and 102 MPa respectively.