With the increasing demand for precision machining in high-end manufacturing, traditional computer numerical control (CNC) machine tool control systems face significant challenges in terms of flexibility and scalability. In response to this issue, this article proposes a design and application scheme for a high-end CNC machine tool main control system based on software architecture. Firstly, this article introduces a modular software architecture to improve the system’s configurability and maintainability; subsequently, the article adopts a task scheduling strategy based on real-time operating systems to ensure the efficiency and stability of system operations; in addition, the article integrates adaptive control algorithms to improve machining accuracy and response speed; finally, the article achieves optimized allocation of hardware resources and construction of a virtual testing environment through virtualization technology. The experimental results showed that compared to hardware-based fixed architecture systems, the research system reduced the total execution time by 41.7% under 100% load, reduced the task loss rate to 15%, reduced the crash rate to 3%, and improved the machining accuracy to 55 μm. Research has shown that the proposed method effectively addresses the application requirements of high-end CNC machine tools in complex machining scenarios, and the software-based architecture has significant advantages in improving system flexibility and scalability.