GdScO ₃and Yb:GdScO ₃single crystals are grown by the chzochralski method in nitrogen atmosphere, and they are characterized by X-ray diffraction(XRD), Raman spectra and transmission spectra . Their lattice parameters, atomic coordinates and temperature factors are determined by Rietveld refinement. It is found that the cell volume of GdScO ₃and Yb:GdScO ₃annealed in air atmosphere increase, but after these sample are annealed in H ₂atmosphere their cell volumes decrease. Based on these results, we demonstrate that the crystal grown in nitrogen atmosphere has interstitial oxygen atoms, and the number of interstitial oxygen atoms in the sample annealed in air atmosphere increases, but that annealed in H ₂atmosphere decreases. The Raman peaks of 155 cm ^–1, 298 cm ^–1, 351 cm ^–1of GdScO ₃are weakened or even disappear when Yb ³⁺ions are doped into it. The Raman spectra of the Yb:GdScO ₃unannealed and annealed in H ₂and air atmosphere are nearly consistent with each other, which indicates that Raman spectrum is insensitive to the defects such as oxygen interstitial caused by annealing. It is suggested that the optical loss of GdScO ₃in the visible wavelength originates mainly from the defect energy level absorption of oxygen interstitial, and transmissivity of Yb:GdScO ₃increases when it is annealed in hydrogen atmosphere, which results from the fact that ytterbium ion can reduce some interstitial oxygen atoms. When GdScO ₃and Yb:GdScO ₃are annealed in air or hydrogen atmosphere, the optical absorption loss of GdScO ₃and Yb:GdScO ₃in a wavelength range of 1000–3000 nm increase due to the trap level produced near the conduction or valence band. The effect on structure and spectral properties of Yb:GdScO ₃and GdScO ₃are explored preliminarily, which is useful for further studying and optimizing laser performance of rare earth doped GdScO ₃crystal.