This paper investigates the relationship among welding process parameters, weld flow viscosity, welding heat generation, finite difference method (FDM) heat dissipation model, microstructural evolution, and mechanical properties during friction stir welding (FSW) of 6061-T6 aluminum alloy. Throughout the study, it was experimentally verified that the temperature inside the weld does not always increase on the AS side compared to the RS side under different welding process parameters, and the highest temperature did not always occur when the stirring pin passed through. As the flow viscosity is dependent on the weld temperature, and viscosity and temperature have corresponding inhibitory and promoting effects on the formation of intergranular structures in the weld, it is shown that the plastic flow of material differs at different positions in the weld nugget, subsequently affecting the macroscopic mechanical properties of the weld.