Entropy is a mathematical expression describing disorder. In this study, the inner dynamics of the city system and the relationship between transportation and urban development are researched with the help of thermodynamics. Self-organizing dynamics reminds us the perfect functioning of city systems. This similarity, leads us to search the problems of cities within their inner dynamic processes. In the theoretical background section of this study; basic concepts concerning thermodynamic equilibrium and their relationships with settlement structures and transport systems will be given. A case study section describes how entropy concept is used to measure dispersion of settlements resulted from transport decisions is given in Ankara, Turkey. A tool for measuring the degree of dispersion in space is developed. With the help of this tool, a model is based on the use of thermodynamic equilibrium and entropy approaches on explaining the dissilience of settlement structures. The results show that the level of entropy in each part of the city is correlated with the energy for mobility and the interventions on zone level influence the overall city system.