GH720Li alloy is the preferred material for aero-engine turbine disk. The morphology, microstructure and micro-area composition of three kinds of γ′ in GH720Li dual-aged alloy were investigated via combination of scanning electron microscope (SEM), transmission electron microscope (TEM) and energy dispersive spectroscope (EDS). γ phases and primary γ′ phases were analyzed by EBSD-EDS method based on the focused ion beam/ electron microscopic system. 3D reconstruction of primary γ′ phases was done by Avizo software. The shapes, morphometric parameters and volume fraction of primary γ′ phases were given by the software and compared with the analysis results of 2D slice. The results show that there are a large number of Σ3 twin boundaries in both γ phases and primary γ′ phases. The primary γ′ phases have multiple shapes from a three-dimensional perspective. The larger continuous primary γ′ phases in three-dimensional space present discontinuous distribution in 2D slice sometimes. The real morphology of primary γ′ phases can be represented comprehensively by 3D EBSD method instead of 2D method. 3D information of primary γ′ provides the basis for heat treatment’s improvement of GH720Li alloy.