A modification of the numerical method of characteristics is developed to solve the initial-boundary value problem that arises when modeling the rectification process in the column. The process is described by a system of first-order hyperbolic equations. A specific peculiarity of the model is in the boundary conditions of a special type. At each of the boundaries, boundary conditions are determined from a system of ordinary differential equations, which also includes unknown values of functions on another boundary. A characteristic difference grid is constructed on the base of a linear transformation of a classical rectangular grid. Implicit second-order difference schemes are used, taking into account the features of the problem at the boundaries. The advantage of this approach is in consideration of the specifics of the propagation of perturbations in hyperbolic equations. Numerical implementation of the method was carried out. An illustrative example shows the effectiveness of the proposed modification of the characterization method. This method is a base for further solution of optimal control problems of flows in columns.