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Diffusion properties of Tm3+ in congruent LiNbO3 crystal have been investigated, together with other two related issues, i.e., Tm3+-doping contribution to refractive index of LiNbO3 substrate and Li out-diffusion. Four X-cut and four Z-cut congruent LiNbO3 substrates locally coated with 15–31 nm-thick Tm-metal films were annealed in surrounding air under different temperatures of 1030°C–1130°C for different durations of 20–70 h. After anneal, refractive index at Tm3+-doped and Tm3+-free parts of crystal surface was measured at the wavelengths of 1311 and 1553 nm and surface Li2O contents were evaluated from measured refractive index. The results show that Tm3+ doping has a weak effect on substrate index and a small contribution to index increment in waveguide layer in comparison with Ti4+- or Zn2+ doping. The Li2O content at the Tm3+-doped surface equals that at the Tm3+-free surface. The Li out-diffusion depends mainly on the diffusion temperature. Below 1100°C, the Li out-diffusion is not measurable. At 1130°C, a 30-h diffusion procedure may cause 0.2–0.3 mol% slight loss of Li2O content. Secondary ion mass spectrometry was used to study the Tm3+ diffusion properties. The results show that the diffused Tm3+ ions in all samples follow a complementary error function profile. From measured Tm3+ profiles, characteristic diffusion parameters such as diffusivity, diffusion constant, activation energy, solubility, solubility constant, and heat of solution were obtained and discussed in comparison with the case of Er3+ diffusion. In comparison with Er3+ diffusion, the Tm3+ diffusion shows similar anisotropy and temperature dependence of solubility. In the aspect of diffusivity, under lower temperature the Tm3+ has a lower diffusivity than the Er3+, and their diffusivity difference reduces with the increased temperature and becomes null at 1130°C.