The Bobbin tool friction stir welding (BT-FSW) process experiment was performed on 2219 aluminum alloy with different butt clearances and misalignments. The maximum allowable clearance and misalignment amount for BT-FSW were obtained, and the weld formation, mechanical properties and microstructure under different parameters were compared and analysed. The results show that the face and back sides of the weld joint surface are perfect and there are no defect inside with the butt clearance under 2 mm and the misalignment under 1.5 mm. During the increase of butt clearance and misalignment, the tensile strength of the weld will be decreased gradually. In comparison, the impact of misalignment on weld strength is lower than that of the butt clearance. The tensile strength from both of them will reach more than 60% of the base metal strength. The lowest hardness value occurs in the thermal-mechanical influence zone, which is 79.1HV, about 70% of the base metal hardness value. The microstructure characteristics are similar to those of conventional friction stir welding. The macroscopic morphology of the welded joint is typical ‘dumbbell type’, and there are many ‘dimples’ in the tensile fracture, which is a typical ductile fracture. A large number of dispersed phase particles (Al2Cu) were found in the dimples, which is the main reason for the decrease in mechanical strength and hardness compared with the substrate.