The dissertation is devoted to the construction and justification of three-point difference schemes of high order of accuracy for solving the Sturm-Liouville problem. A new algorithmic realization of the exact three-point difference scheme on a non-uniform grid has been developed. We show that to compute the coefficients of the exact scheme in an arbitrary grid node, it is necessary to solve two auxiliary Cauchy problems for the system of three linear ordinary differential equations of the first order. The coefficient stability of the exact three-point difference scheme is proved. If the Cauchy problems are solved numerically using any one-step method, we obtain the truncated three-point difference scheme. The accuracy estimate of three-point difference schemes was obtained and the algorithm for finding their solution was developed. We also developed a new algorithmic realization of the exact three-point difference scheme for the Sturm-Liouville problem with singularities at the ends of the interval. As in the case of the classical Sturm-Liouville problem, to find the coefficients of the exact three-point difference scheme, it is necessary to solve two auxiliary Cauchy problems for each grid node. The coefficient stability of the exact three-point difference scheme is proved. Since the Cauchy problems for the first and last grid nodes are singular, the Taylor series method has been developed to solve them. The accuracy estimate of truncated three-point difference schemes was obtained. To solve the difference scheme, the Newton's iterative method is used. Numerical experiments are presented which confirm the efficiency of the proposed approach.