The article considers the features of transport as an object of technological innovation, due, on the one hand, to the service nature of the main activity and the specifics of innovative processes during provision of transport and logistics services, and, on the other hand, to the high capital intensity and technological complexity of the infrastructure transport complex, which is the focus point of technological innovation.The objective of the article is to substantiate the initial prerequisites for developing an alternative approach to making strategic decisions on development of transport organisations based on technological innovations, which, besides the traditional justification of economic efficiency, considers several non-economic factors. The method of substantiation is a systemic strategic analysis, which allows to study the features of the transport complex in the context of the factors of external environment and their dynamics.Regarding the Russian Federation, the scale of the national territory, natural and climatic diversity and uneven territorial distribution of the resource and production base determine the special role and place of transport in the national economy, which quite often leads to the need to make decisions on development of the transport complex based on predominantly non-economic factors (such as security, reliability, environmental friendliness, etc.) and on scientific, technical, political and socio-economic forecasts. At the same time, private enterprises (with or without participation of the state) dominate currently almost all transport sectors where they operate on the principles of profitability, investment attractiveness and competitiveness, which leads to inconsistency of internal decision-making criteria in the field of technological strategies.The ongoing change in the technological paradigm is an additional and significant factor determining trends in transport developments. It is based on the processes of digitalisation and digital transformation of the transport and logistics business. The problems of decision-making in implementation of technological innovations in transport industry, arising from its peculiarities, necessitate a revision of approaches since economic assessments of efficiency are not always able to reflect the real needs and feasibility of choosing mainstream trends in technological development of the transport system.The analysis of the features of the transport and logistics industry based on universal experience and cases in Russian practices in the context of formation of a new technological paradigm makes it possible to substantiate the methodology for making strategic decisions on implementation of technological innovations.