The invention discloses a pneumatic control system and method for a square ball valve automatic assembly workbench. The pneumatic control system comprises an air source, a controller, a valve body clamping control system, a valve cover tightening control system, a valve element air inflating control system and a disassembly control system; a four-jaw chuck is driven by a pneumatic motor to clamp a valve body, a main transmission connector is driven by an electric machine to tighten a valve cover, a valve element is inflated by an external air source through a pneumatic one-way valve, and the pneumatic motor is driven by air pressure provided by the air source to rotate so as to close the valve element; disassembling is conducted after assembling of a square ball valve is finished, so that unloading of clamping force of the valve body is achieved through the reverse rotation of the pneumatic motor; in the pneumatic control system, the assembling process is monitored through a torque sensor and a flow sensor, and precise controlling is conducted on all assembling processes through the controller. According to the pneumatic control system and method for the square ball valve automatic assembly workbench, the continuousness of the steps such as automatic clamping, assembling, air inflating and disassembling in the square ball valve assembling process is achieved, and the automatic assembling effect is achieved, the assembly quality of products is stabilized, and the labor intensity of manpower is reduced.