A method for determining the two-dimensional (2D) index profiles of channel waveguides by the datum of the effective indexes measured by prism coupling method is proposed. The channel waveguides are home-fabricated by ion-exchanged method on the substrate of phosphate glass with various diffusion times and various mask opening widths. The method for calculating the 2D index profiles is set up based on the theory of graded-index waveguides,such as Wentzel-Kramer-Brillouin (WKB) method and effective index method. First,an index profile function is supposed. Then its effective indexes calculated by a homemade program based on WKB method and effective index method are compared with the measured results of the effective index. Finally the best-fit index profile is reconstructed by modifying the supposed index profile until the calculated effective indexes are becoming very close to the measurement of the effective indexes. The relationships between the fabricating parameters,such as diffusion time and mask opening width,with index profile of waveguides can be set up. This work could be useful for optimizing the fabrication process of channel waveguides in order to obtain high quality waveguide lasers and photonic waveguide devices repeatedly and effectively.