The article describes the uses of multi-input/multi-output systems, with the aim of assessment of structural changes and stability in the Russian transport sector. Empirical input-output data for the period between the years 2000 and 2014 are used. A basic model and overview of the literature are given. The article summarizes the assessment of structural changes and stability. The author gives his own vision of a state of the Russian transport sector. The analysis is carried out for the transport sector as a whole as well as for the various transport modes. Analytical and quantitative results are presented. Assessments of the dynamics of several key economic indicators of the Russian transport sector based on the model calculations are discussed. The indicators were compared based on World Input-Output Database (WIOD) version 2016. It is shown that the share of intermediate goods and services in the transport sector’s gross output fell, while the share of final goods increased from 2000 to 2014. But the share of air transport in the transport sector’s gross output as a whole was stable in 2000-2014.