The relevance of the problem stated in the article is that in conditions of nonstationary economy the modification of existing approaches and methods is necessary during the formation of the capital. These methods allow taking into account the heterogeneity of factors' change in time and the purpose of the development of a particular company, thereby ensuring higher market value of the business. The purpose of this article is to develop a methodology for determining the risk associated with the formation of the capital structure in conditions of nonstationary economy. During the study, the authors used the methods of economic-statistical and factor analysis, economic and mathematical modeling, allowing to consider the problem as a purposeful and organized process and form the capital structure with the objectives of business development, the dynamics of changes in each component of the cost of capital, minimize total financial costs and risks to attract sources for the foreseeable future and to maximize the market value of the company. The methodology includes five stages: creation of a dynamic database of key macro and microeconomic indicators; the formation of the matrix of the risk reasons associated with the price of capital, the calculation and comparative analysis of factors affecting the cost of capital in a period of time; establishing a weighted average cost of capital and its components for the planning period and determining the degree of influence of each component on the price change of capital and total risk level. The proposed methodology of the evaluation of the capital structure can be used in conditions of nonstationary economy for companies engaged in activities at the expense of their own and borrowed funds, considering the cost of capital by the current time.