The design of welding tool is a critical key for alleviating the heterogeneity of the long-thick plate friction stir welding (FSW) joints. In this work, two types of segmented composite-shaped pins were developed, and their effects on microstructural and mechanical properties heterogeneity of 7050-T7451 aluminum alloy long-thick plates (900 mm long and 12.7 mm thick) were investigated. Compared with the two-stage tool (T1), there is the eliminates the formation of loose zone generated by the three-stage-tool (T2), due to the more proper axial movement of the plastic metal. The improved plastic deformation and strain rate facilitate enhanced dynamic recrystallization and grain refinement in the T2 joint. Benefiting from the elimination of the loose zone of the weld nugget zone and a more homogeneous microstructure, the T2 joint exhibits improved and more narrowly distributed mechanical properties across its slices. The T2 joint demonstrates a 1739 % increase in ultimate tensile strength (UTS) and a 271 % increase in elongation, while the coefficient of variation (CV) for yield strength (YS), UTS, and elongation decreases by 81 %, 31 %, and 53 %, respectively. The findings will provide a valuable and effective strategy for achieving superior and more homogeneous long-thick plate joints.