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. With an extended treatment time of DCT, the microhardness of the welded joints reaches its peak, leading to an average microhardness increase of up to 6.9% compared to welded joints without DCT. Additionally, the tensile properties of the welded joints reach 385.3MPa, marking a 7.4% increase in tensile strength compared to joints without DCT. These experimental results underscore the significant impact of DCT on improving the welded joints.