In order to meet the development needs of solid-state lasers, it is necessary to continuously improve the YAG laser crystal growth technology. However, controlling the defect structure in YAG is particularly difficult for crystal development in industry and scientific research. The defects of crystal samples prepared by the two processes were studied, especially the origin of crystal scattering points. Positron annihilation technology (PAT) is a sensitive and effective nuclear technology for analysis and characterization method being used to control microstructure of materials, which is extremely sensitive to vacancy defects and micropores. According to the PAT analysis results,the positron annihilation lifetime spectrum and Doppler broadening spectrum, the positron lifetimes and line-shape parameters of Doppler broadening spectra of samples vary with different processes and with or without scattering points indicating that the main defects of the crystal are the intrinsic defects in the YAG structure.The scattering points may be nanopores caused by vacancy agglomeration, indicating that the PATis very sensitive to characterize the scattering points in the YAG crystal. The present experimental results of positron annihilation are consistent with the results of single crystal quality reflected by X-ray diffraction (XRD), single crystal rocking curve (XRC), optical transmittance, and dislocation density, indicating the uniqueness and technical advantages of positron annihilation technology in studying the relationship between physical properties and defects/microstructure of crystal materials. Meanwhile, it can be concluded that the PAT can effectively reflect the crystal quality at micro scale.