Logistics system is one of the basic concepts of effective supply chain management. In the Republic of Kazakhstan, all types of public transport constitute a single transport system (ETS), which includes railway, river, sea, road, air and pipeline transport. An important element of the ETS of the country is the transport network, which determines the possible directions of transportation and the points between which a particular type of communication is established. It consists of communications of different types of public and non-public transport. The formation of effective supply chain management and transport network is due to a number of socio-economic factors: the development and location of the economy; urban settlements; the direction and power of the main transport and economic relations; location of large resort and tourist sites, the need to optimize costs. Additionally, this research analyzes the trends in innovation for logistic services of supply chain management in the targeted region through multiple aspects, intellectual capital, and organizational resources. Research findings show that both multiple aspects and intellectual capital are positively and significantly associated with innovation in logistic services for the supply chain management. However, the study finds no evidence for the relationship between organizational resources and innovation for logistic services in supply chain management. As a result of the research, practical aspects and significance of the management of the transport and logistics system of the republic are determined, on the basis of which the relevant conclusions were made.