In order to improve the comprehensive mechanical properties of the welded joints of the 5A06 aluminum alloy, friction stir welded (FSW) joints were subjected to deep cryogenic treatment (DCT). The microstructure and mechanical properties were characterised using metallographic microscopy, x-ray diffractometer (XRD), energy spectrometer, microhardness tests, and tensile tests. The experimental results show that DCT refines the structure significantly due to the large temperature difference. This refinement results from an increase in Mg atoms within the α-Al solid solution through the precipitation of Al atoms, forming the Al3Mg2 phase. This enhancement in plasticity is achieved through dispersion distribution. Moreover, as the treatment time of DCT increases, the mechanical properties of the welded joint also improve significantly. The microhardness of the welding joint peaked at DCT3h, rising from 78.8 HV at DCT0h to 87.2 HV at DCT3h. Meanwhile, the tensile strength of the joint reached its maximum at DCT12h, rising from 358.7 MPa at DC0h to 385.3 MPa at DCT12h, representing a 7.4% increase. These experimental results underscore the significant impact of DCT on improving the welded joints.