The article describes the structure of the Russian economy by sectors, which should be choosen as the regions with the highest gross regional product (GRP). The dynamics of the indicators characterizing the efficiency of the Russian economic development is considered. The impact of the economic sectors and structural shifts on the indicators is assessed. The production functions connecting the main indicators of economic development are constructed for each sector. To study the influence of the meso-level on the macro-level the models, enabling to connect the parameters of the equations of different levels and assess the effect of the structural shifts on the economic efficiency indices, are built. Based on the proposed approach the optimal structure of the Russian economy is defined with certain limitations. The obtained results were compared with the pre-reform period. The research results show that the influence of the structural shifts on the rates of economic growth was the highest in the middle of the 1990s comprising 2 – 3%. Then it dropped down to 0%, slightly increased to 0.2% in 2003–2004 and became negative after the year 2007. Moscow had the biggest impact on the efficiency. An average of 16% of the labor productivity growth in the Russian Federation was connected with the development of the Moscow economy, yet in some periods its value reached up to 40%. The impact of the regions on the elasticity in respect to the funds slightly differed. The impact of Moscow turned out to be unexpectedly high, reaching an average of 65% in the 1990s and 30% in the 2000s. The calculations showed a lack of the optimal investment allocation, which was probably due to the pre-reform policy and the policy of 2000s aimed at the preservation of certain production proportions and support of the weak regions.