GdScO₃ and Yb:GdScO₃ single 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 GdScO₃ and Yb:GdScO₃ annealed in air atmosphere increase, but after these sample are annealed in H₂ atmosphere 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 H₂ atmosphere decreases. The Raman peaks of 155 cm^–1, 298 cm^–1, 351 cm^–1 of GdScO₃ are weakened or even disappear when Yb³⁺ ions are doped into it. The Raman spectra of the Yb:GdScO₃ unannealed and annealed in H₂ and 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 GdScO₃ in the visible wavelength originates mainly from the defect energy level absorption of oxygen interstitial, and transmissivity of Yb:GdScO₃ increases when it is annealed in hydrogen atmosphere, which results from the fact that ytterbium ion can reduce some interstitial oxygen atoms. When GdScO₃ and Yb:GdScO₃ are annealed in air or hydrogen atmosphere, the optical absorption loss of GdScO₃ and Yb:GdScO₃ in 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:GdScO₃ and GdScO₃ are explored preliminarily, which is useful for further studying and optimizing laser performance of rare earth doped GdScO₃ crystal.