The effects of welding layer arrangement on the microstructure and mechanical properties of 5083/6005A aluminium alloy gas metal arc welded (GMAW) joints were studied. High-quality butt joints were obtained under different welding layer arrangements, including two layers and two passes, two layers and three passes, and three layers and three passes. The results indicated that the softening zone located in the heat-affected zone (HAZ) of the 6005A aluminium alloy side was the weakest part of the 5083/6005A alloy joints. The highest level of recrystallization and precipitate dissolution was observed in the HAZ of the two-layer and two-pass joints; however, the lowest level was verified in the three-layer and three-pass joints. With the increase in the number of welding layers and passes, grain boundary liquation in the partially melted zone (PMZ) and strength loss of the softened zone were improved. The tensile strength of the two-layer and two-pass joints was 161 MPa, while that of the three-layer and three-pass joints increased to 217 MPa.