Using cold spraying (CS), a surface layer with a modified microstructure and enhanced mechanical properties was formed on a 3.2 mm thick friction stir welded (FSW) AA2024-T3 joint. The combined effect of “shot peening effect (SPE)” and “heat flow effect (HFE)” during CS were used to enhance joint mechanical properties. The microstructure evolution of the FSW AA2024-T3 joints in the surface layer following CS coatings and their effect on mechanical properties were systematically characterized with electron back-scattered diffraction, transmission electron microscopy, differential scanning calorimetry and mechanical tests. Based on these experiments, a grain refinement, finer and more S phases, and improved amount of Guinier-Preston-Bagaryatsky (GPB) zones produced by CS treatments are proposed. The deposition of aluminium coating on the joint, lead to hardness recovery in the stir zone and the development of two low hardness zones as the density of GPB increased. The tensile properties of FSW AA2024-T3 joints improved with the application of the aluminium coatings. Experiments and analysis of the enhanced mechanical properties mechanism indicate that SPE with a high plastic deformation and HFE with an intensive heat flow are necessary for the production of refined grains and increased numbers of GPB zones.