With the development of industrial manufacture in the context of Industry 4.0, various advanced technologies have been designed, such as reconfigurable machine tools (RMT). However, the potential of the latter still needs to be developed. In this paper, the integration of RMTs was investigated in the capacity adjustment of job shop manufacturing systems, which offer high flexibility to produce a variety of products with small lot sizes. In order to assist manufacturers in dealing with demand fluctuations and ensure the work-in-process (WIP) of each workstation is on a predefined level, an operator-based robust right coprime factorization (RRCF) approach is proposed to improve the capacity adjustment process. Moreover, numerical simulation results of a four-workstation three-product job shop system are presented, where the classical proportional–integral–derivative (PID) control method is considered as a benchmark to evaluate the effectiveness of RRCF in the simulation. The simulation results present the practical stability and robustness of these two control systems for various reconfiguration and transportation delays and disturbances. This indicates that the proposed capacity control approach by integrating RMTs with RRCF is effective in dealing with bottlenecks and volatile customer demands.