Friction Stir Welding (FSW) is an advanced solid-state joining technique that utilizes a rotating tool to generate frictional heat, facilitating plastic deformation for material consolidation. This process ensures defect-free joints while maintaining structural integrity, making it a preferable alternative to conventional fusion welding, especially for aluminum alloys with poor weldability. In this study, the microstructural characteristics of FSW joints in homogeneous and heterogeneous aluminum alloys (AA2024 and AA7075) are analyzed. The mechanical properties of the weld are influenced by the base materials at the advancing side (AS) and retreating side (RS). Microstructural evaluation reveals particle coarsening in critical regions, including the thermo-mechanically affected zone, nugget zone, and heat-affected zone. Variations in chemical constituents result in different peak intensities due to crystallographic changes. These effects are observed across the heat-affected zone, thermo-mechanically affected zone, and base material regions on both the advancing and retreating sides in dissimilar FSW joints. The findings contribute to a deeper understanding of microstructural evolution in FSW, aiding in process optimization for enhanced joint performance.