The application of cryogenic helium systems is presently limited because the unattended automatic operation of helium purifiers, which are essential components, has not been fully implemented. The present study addresses this issue by designing and implementing a control system for an automatic dual-cylinder helium purifier consisting of two independent purification systems that share a common regeneration, evacuation, and helium purification infrastructure. The automatic control system implements data acquisition and storage, temperature control, logic computing, and flow rate control and monitoring operations based on a commercially available controller and a touch screen serving as the human-machine interface. The control system coordinates the use of the common infrastructure by the independent purification systems via the implementation of a completely automatic time-division multiplexing process, and the operating states and other essential conditions of the entire control system are monitored separately in real time. The human-machine interface also implements fully manual and semi-automatic control of the separate purification systems.