This chapter introduces system-level modelling methods for simulation and optimisation of energy systems integrated with thermal energy storage (TES) technologies. Due to increasing interest in development, operation and control of systems coupled with TES a number of modelling methodologies have emerged. These methods can be of great benefit in assessing the performance, costs and value of the integration of TES into systems and processes before the construction of physical installations. The chapter discusses also how process modelling methods, black-box modelling methods and data-driven methods are mathematically formulated and applied to energy systems with TES. Furthermore, discussion is also made on the coupling of system-level modelling methods with TES sub-models to perform simulations and optimisation of integrated systems. Finally, selected applications of modelling methodologies are presented for each of the TES technologies.