The master station programming tool is an important component of the visual design， download， and operation of the whole logic function and motion control function programs of a programmable control system. To break the foreign monopoly on industrial control software platforms， the development of a safe and reliable master station programming tool serving an autonomously controllable， programmable， control system， is paramount. This paper investigates the design method for each component of the master station programming tool chain. First， according to the working principle of an open-source integrated development environment （IDE）， a software architecture for the master station programming tool based on IEC61131-3 is proposed. Then， the plug-ins for bus configuration and data access in the IDE are designed from the perspective of generating code integrity， and the architecture and components of Runtime executed by the master code are also designed， forming a fully functional programming tool chain. Finally， taking two basic safety functions as examples， the integrated development method of the IEC61800-5-2 functional safety basic library is analyzed. The experimental results show that the master station programming tool designed in this paper has functions such as visual programming， downloading， and running， and it meets the basic program development requirements for autonomously controllable， programmable， control systems.