The article examines the essence of the concept of such terms as security and economic security of the transport system of the region, and analyzes the existing approaches to the interpretation of the concept of "economic security". The author's definition of the concept of "economic security of the region" is proposed as a set of conditions and factors aimed at ensuring a fair and adaptive economic environment, conducive to innovation, sustainable development, ensuring an adequate standard of living of the population, with the ability to withstand threats of any nature. Comparative characteristics of methods for assessing economic security are carried out. A method for assessing the level of economic security of the transport system of the region is proposed, which is based on the study of the value of the basic indicators of the economic security of the transport system of the region, with the calculation of integral indicators of economic security. The basic indicators of the economic security of a separate region are given in a comparable form by normalizing them relative to the average values for all territories of the country. The standardization of basic indicators for assessing the state of economic security of the transport system of the region is proposed. Economic security was assessed by calculating the integral coefficient, by the method of multivariate comparative analysis. To assess the economic security of the transport system of the region, a group of indicators of personnel, financial, transport, energy, production and technological, scientific and technical, informational, environmental safety was used, allowing to get an idea of economic security in general. For each safety indicator, the best (reference) value is determined, which is taken as a unit, then the indicators for each safety component are compared with the standard.