The influence of different annealing conditions on refractive index profiles of He and H ions implanted lithium niobate planar waveguides have been studied. After annealing treatment with different time and different temperature the dark modes of both kinds of waveguides were measured by using a prism coupling method. The refractive index profiles of both waveguides before and after annealing treatment were given. The results show that both He and H ion implantation result in the decrease of the ordinary refractive index in barriers, but in the region of guides the extraordinary refractive index increases. Annealing treatment influences the ordinary refractive index profiles obviously, but under 400 °C the annealing treatment almost has no influence on the extraordinary refractive index profiles.