The article proposes a methodological approach and algorithmic tools for the simulation modelling of a transport and logistics system operating under the specified conditions. The method is based on the formalisation of a system of circular routes for ice-class vessels and linear icebreakers using a discrete vector representation, which transforms the cyclic structure into a linear one in order to simplify computational procedures. To automate the labour-intensive process of preparing initial data, a special algorithm has been developed which, based on a graphical representation of routes and the application of a wave algorithm, constructs their complete coordinate-by-coordinate description and forms the discrete working vector of the model. This makes it possible to minimise manual input errors and ensure the reproducibility of experiments. The model simulates the key technological processes: vessel movement along routes, queue formation at roadsteads at the points where icebreaker assistance begins, the formation of “icebreaker–vessel” pairs, and their joint movement along the ice-covered section. The target indicators used to analyse various scenarios include the total voyage cycle time, queue waiting time, icebreaker fleet utilisation, and the overall carrying capacity of the system. The practical significance of the study lies in the creation of a tool for multivariate analysis and synthesis of the parameters of the Arctic logistics chain. The model makes it possible to provide quantitative justification for decisions on the optimal composition and number of LNG carriers and icebreakers, to assess the influence of navigational conditions on the regularity of deliveries and, consequently, to improve the validity of strategic investment and operational management decisions for projects such as Arctic LNG 2. The developed approach contributes to the advancement of methods for planning sustainable and cost-effective transportation in the Arctic zone of the Russian Federation.