The use of approaches and methods of mathematical analysis to the selection and justification of sources of financing for an innovative project is an important and urgent task. The approach presented in the paper is based on a system of equations that allow determining the optimal capital structure necessary to finance an innovative project. This system of equations, using methods of mathematical analysis, provides the best effect of financial leverage. The use of this methodology in the activities of commercial organizations is a modern practical tool necessary for the effective functioning of the decision support system.