Historically, researchers and managers have often failed to consider organizations as a sum of functions leading to a set of capabilities that produce a product that can serve society’s needs. Furthermore, functions have increased with the development of industrial revolutions, however, many manufacturing organizations have not realized their full potential. As a result, many industrial organizations do not know why, where, and when the existing functions and projects for implementing new functions fail where tactical and strategic functions of a manufacturing organization are commonly over-seen. Thus, the aim of this research was to propose a holistic approach for manufacturing organizations in order to model their functions enabling the assessment, design, management, and control of operations and performance as well as to identify improvement potentials. For this purpose, a conceptual model was developed based on the evolution of functions along with the industrial revolutions. Moreover, using the conceptual model, manufacturing organizations can be modeled, considering common organizational functions in the respective areas of production, maintenance, and quality, etc., in the three planning horizons—strategic, tactical, and operative. As a result, the model serves as a basis for the integral management and control of manufacturing organizations. Moreover, it can be also used as a basis framework for a digital twin model for organizations. Thus, a system dynamics simulation model based on the conceptual model was developed for a generic organization. The goal of the simulation model is to provide an exemplary digital model of a manufacturing organization in which the different functions are applied with different methods, systems, and/or individuals along the development phases.