Structural materials with high strength-to-weight ratio are the candidate materials for future automotive applications. In this attempt, thick dissimilar AA6061/AA2014 alloys were welded by friction stir welding. This experiment aims at investigating the effect of polygonal hybrid pin profiles on structure–property relationship. The effect of tilt angle and tool offset on material flow at nugget zone was also investigated. The weld joint characterisation was done by optical microscopy, SEM and XRD to reveal the microstructure and constituent elements in the weldment. The weld profile produced by polygonal pin exhibits equiaxed fine grains at nugget zone. The characteristic study of tensile strength, micro-hardness and flexural strength was carried out. Optimum weld condition was found at a tool rotational speed of 900 rpm, weld speed of 20 mm/min, tilt angle of 1°, tool offset of 1.5 mm and with hybrid square pin profile. © 2020, © 2020 Engineers Australia.