Nowadays, the concept of Industry 4.0 aims to improve factories’ competitiveness. Usually, manufacturing production is guided by standards to segment and distribute its processes and implementations. However, industry 4.0 requires innovative proposals for disruptive technologies that engage the entire production process in factories, not just a partial improvement. One of these disruptive technologies is the Digital Twin (DT). This advanced virtual model runs in real-time and can predict, detect, and classify normal and abnormal operating conditions in factory processes. The Automation Pyramid (AP) is a conceptual element that enables the efficient distribution and connection of different actuators in enterprises, from the shop floor to the decision-making levels. When a DT is deployed into a manufacturing system, generally, the DT focuses on the low-level that is named field level, which includes the physical devices such as controllers, sensors, and so on. Thus, the partial automation based on the DT is accomplished, and the information between all manufacturing stages could be decremented. Hence, to achieve a complete improvement of the manufacturing system, all the automation pyramid levels must be included in the DT concept. An artificial intelligent management system could create an interconnection between them that can manage the information. As a result, this paper proposed a complete DT structure covering all automation pyramid stages using Artificial Intelligence (AI) to model each stage of the AP based on the Digital Twin concept. This work proposes a virtual model for each level of the traditional AP and the interactions among them to flow and control information efficiently. Therefore, the proposed model is a valuable tool in improving all levels of an industrial process. In addition, It is presented a case study where the DT concept for modular workstations underpins the development of technologies within the framework of the Automation Pyramid model is implemented into a didactic manufacturing system.