The use of a digital twin as an enabling technology for industry 4.0 provides control systems engineers with novel tools for modelling, designing, and controlling complex systems, providing a deep understanding of the physical asset based not only on its physics but also the real system’s response. It is particularly critical for uniformity temperature control applications, where providing a reasonable model of the system’s diffusion is always affected by the physical behavior of the system’s components required for heating, cooling, or power distribution. In this paper, a digital twin is used to represent a multivariable thermoelectric system employed for temperature uniformity distribution control with potential applications in semiconductor manufacturing. The modelling employs a five-step methodological framework consisting of the stages: target system definition, system description, multiphysics and data-driven simulation, behavioral matching, and implementation to represent the system’s temperature distribution accurately. The temperature distribution is measured using an infrared thermal camera to perform model behavioral matching on heating and cooling temperature uniformity applications. The obtained results indicated that using digital twins not only increases the accuracy of the system’s representation but can also provide the system with novel information that can be leveraged for the design and implementation of smart control systems.