As a new type of grain refiner, rare earth element Sc has a strong grain refining effect on the microstructure of cast aluminum alloys. During the solidification of Sc-containing aluminum alloys, Al3Sc particles are formed in the molten metal and act as heterogeneous nucleation cores of Al in the nucleation process, which significantly increases the nucleation rate and refines the grains. In this paper, a focused ion beam (FIB) microscope was used to extract Al3Sc particles from an Al-Sc alloy, and the internal structure of the particles was systematically observed. At the same time, a scanning electron microscope (SEM) and high-resolution transmission electron microscope (HRTEM) were used to study the morphological characteristics of particles and the crystallographic orientation relationships (ORs) at the interface. The study found that under the influence of strong anisotropy, the growth rate of Al3Sc crystal high-index crystal plane and low-index crystal plane is significantly different. In the process of crystal growth, the high-index crystal planes grow faster and disappear quickly, and the shape of the crystal can be ultimately determined by the slower-growing low-index crystal planes. Inside the Al3Sc particles, the (111) and (110) planes form coarse dendritic structures, the (100) planes form a large number of fine cell structures, and there are white oxide residues in the center of some particles. At the interface between Al3Sc and Al matrix, two parallel crystallographic ORs were observed, and the atomic arrangement on both sides of the interface was found to be consistent. At the same time, a special pseudomorphic solid (PS) layer was observed at the interface. On the (111) crystal plane, the atomic arrangement of the PS layer was consistent with Al3Sc at an angle of 60° with Al.