During friction stir welding, the nugget zone (NZ) underwent severe plastic deformation and high temperature. This process resulted in high density of dislocations and dissolving of the precipitation. In this study, the stored energy of the NZ in friction stir welded Al-Mg-Si joint was quantitatively analyzed by means of differential scanning calorimetry (DSC). The microstructure of the NZ was investigated by electron back scattering diffraction (EBSD) and transmission electron microscope (TEM). DSC analysis showed that the energy stored in the NZ was about 8.565 J/g. Microstructure investigation showed that the NZ was composed of low-angle grain boundary (42%) and high-angle grain boundary (58%). Meanwhile, there were high density dislocations in the NZ. The stored energy was quantitatively analyzed based on EBSD data and dislocation density. The results showed that the stored energy resulting from the grain boundary and dislocations was about 0.0247 J/g and 0.0712 J/g, respectively. These results proved that the precipitation played dominant role in stored energy while the contribution of grain boundary and dislocations are negligible.