This paper presents an application of an open architecture control system implemented on a multi-axis wood computer numerical control milling machining center, as a digital twin control. The development of the digital twin control system was motivated by research and educational requirements, especially in the field of configuring a new control system by “virtual commissioning”, enabling the validation of the developed controls, program verification, and analysis of the machining process and monitoring. The considered wood computer numerical control (CNC) machining system is supported by an equivalent virtual machine in a computer-aided design and computer-aided manufacturing (CAD/CAM) environment, as well as in the control system, as a digital twin. The configured virtual machines are used for the verification of the machining program and programming system via machining simulation, which is extremely important in multi-axis machining. Several test wood workpieces were machined to validate the effectiveness of the developed control system based on LinuxCNC.