In this study, static shoulder friction stir welding (SSFSW) is innovatively employed to join Al6061 and Ti6Al4V, aiming to minimize material mixing and intermetallic formation, significantly influencing the interfacial microstructure and joint strength. The results revealed that SSFSW reduced the intermetallic layer thickness at the interface, improving joint quality. The mutual interdiffusion of Al and Ti at the interface was influenced by an exothermic chemical reaction, forming an Al5Ti2–Al3Ti sequence due to the diffusion of Al into the Ti matrix. The microstructural analysis demonstrated better interfacial microstructural homogeneity in SSFSW joints than conventional FSW (CFSW), with finer titanium particle distribution. The larger particles resulted in coarser grains in CFSW, affecting the mobility of dislocations, which potentially led to the inhomogeneous concentration of dislocations at the interface. Recrystallization mechanisms varied between CFSW and SSFSW, with the Ti interface showing equiaxed and recrystallized grains due to the dynamic recovery driven by adiabatic shear bands. The tensile testing results of SSFSW exhibited a joint efficiency of 88%, demonstrating a 20.2% increase compared to CFSW, which can be attributed to differences in fracture modes. This study contributes to an understanding of dissimilar Al-Ti joining and provides insights for industries seeking to leverage the benefits of such combinations in lightweight and high-performance structures.