The article analyzes oil and gas industry as one of the most important sectors of the Russian economy accounting for a large share of GDP. The effectiveness of the integrated company’s management system in the oil and gas industry depends largely on the effectiveness of the company’s organizational structure. Most integrated oil and gas companies in Russia are known to have an excessive concentration of management functions at the highest level – the CEO and his staff. Therefore, before introducing modern management systems into integrated oil and gas companies, it is necessary to carry out a structural reorganization to ensure the transition to a matrix or multi-divisional organizational management structure based on a new conceptual approach to management system modernization, and singling out the development subsystems.