Over recent decades, the demand for smarter and more intelligent manufacturing systems has increased in order to meet the growing requirements of customers. Manufacturing systems are termed as smart manufacturing systems (SMSs); these systems are capable of fully integrated autonomous operation. Specifically, the concept of autonomous systems and functions has been adopted for next generation manufacturing systems (NGMSs). Among these NGMSs, the fractal manufacturing system (FrMS) exhibits several characteristics that are similar to those of SMSs. Therefore, in this paper, a smart, self-reconfigurable manufacturing system (SSrMS) based on the FrMS is proposed. The proposed SSrMS architecture was designed for realizing self-reconfiguration functions based on the FrMS concept. SSrMS exhibits a fractal structure, which enables the distribution of control features; this also constitutes the fundamental basis of autonomous operation and reconfiguration between each fractal. SSrMS architecture includes the use of big data, digital facilities, and simulations. Furthermore, we introduce three reconfiguration methods to conduct system reconfiguration, which are a goal decision model, a negotiation model, and a sustainability assessment method. The goal decision model was developed to determine a goal of each fractal to achieve the system’s goal. In other words, each fractal can decide a goal to achieve the system’s goal, such as maximizing productivity or profit, or minimizing cost, and others. The negotiation model was adopted to perform partial process optimization by reassigning tasks and resources between the fractals, based on the goal of coping with the changes in the system’s condition. The sustainability assessment method was designed to simultaneously evaluate sustainability with respect to the system’s goals. The proposed architecture of SSrMS with goal decision model, negotiation model, and sustainability assessment method has the features of self-optimization, self-organization, and self-reconfiguration in order to achieve fully autonomous operations for the manufacturing system. The proposed architecture including three methods are expected to provide a fundamental study of the autonomous operations. The main findings of in this study is the development of a new architecture for fully autonomous operations of the smart manufacturing system with reconfiguration methods of goal-oriented manufacturing processes.