The modern economy of the Russian Federation is constantly facing crisis phenomena at various levels. At the macro level, it is the absence or low GDP growth rate, the critical dependence of the economy on oil and gas exports, the volatility and undervaluation of the exchange rate, the small share of the manufacturing industry and the prolonged destruction of its fixed assets, the dependence on external sanctions, corruption. In all cases, this is the inefficiency of governance mechanisms. The problems of the development of the transport complex as an important component of the Russian economy, ensuring the balance of output of the construction and other types of economic activity were considered. Indicators of productivity potential, equilibrium index, output limits, indicative increments of output of branches are used to assess the influence of the transport complex component on the basis of the «input-output» model. Methods for analyzing the mechanisms of managing the developing economy systems are considered. On the basis of the model of the economic system in the mode of autonomy, methods of assessing productivity indicators have been developed. The procedure for calculating indicative dynamics of volume proportions of output for autonomous mode is considered. An example of the calculation results for the structure of the inter-industry balance of the Russian Federation is given.