LiNbO3 crystal with a lithium composition gradient of Li/Nb = 0.8 wt%/cm (Li0.97..1.01Nb1.03..0.99O3) were obtained. A monotonic change in the edge of the UV absorption edge is observed when scanning the surface of the gradient crystal along the growth direction. Raman spectra from different areas of studied crystal were analyzed in a wide frequency range, which includes the region of fundamental vibrations of the crystal lattice (100–900 cm−1) and the region of overtone processes (900–3000 cm−1). A compositionally homogeneous, congruent LiNbO3 crystal was used as a comparison sample. It was found that in the spectra obtained from different parts of the gradient crystal, there is a significant scatter in the frequency values of the lines corresponding to the fundamental vibrations of the crystal lattice, but at the same time, the number of lines corresponding to the fundamental vibrations of the lattice for the gradient and compositionally homogeneous LiNbO3 crystals is the same. Moreover, in the spectrum of a gradient crystal in the region of overtone processes of fundamental vibrations, significantly more lines (35 lines) are observed than in the spectrum of compositionally homogeneous crystals (15 lines). The data obtained show that the state of the defect structure of compositionally homogeneous crystals and gradient LiNbO3 crystal is significantly different. The discovered differences between the defective structure of a gradient crystal and the defective structure of a compositionally homogeneous crystal may be the reason for compensation (damping) of distortions during nonlinear optical conversion of laser radiation by a gradient crystal due to the uneven temperature distribution along the length of the crystal. In compositionally homogeneous crystals, such temperature distortions significantly limit the efficiency of nonlinear optical conversion.