Lap joint friction stir welding (FSW) between dissimilar 5052-H112 (1 mm) and 6061-T6 (2 mm) Al alloys with different thickness was carried out with various tool rotation speeds and welding speeds according to the fixed location of each material on bottom or top sheet. Interface morphology was characterized by pull-up or pull-down from initial joint line. Amount of vertical material transports increased and thickness of 5052 resultantly lessened with increasing tool rotation and decreasing welding speed, which were the conditions of the weak bond. Higher stress concentration on the interface pull-up region, the penetration of unbonded region into the weld zone and the lessened thickness of 5052 Al part might be the reasons for lower fracture load. Higher fracture load was acquired at the lower tool rotation speed and higher welding speed when a thicker 6061 was fixed at retreating side on top sheet. Interface morphology was the most important factor determining the mechanical strength of lap FSW joints and can be manageable using FSW parameters.