The control system for the ion source of the JUNA（Jinping Underground laboratory for Nuclear Astro-physics) was designed and implemented. It is built by using a distributed system model. The hardware adopts PLC, serial device server, servo motor, industrial computer, and other components to realize the remote monitoring and controlling of ion source devices. The software integrates all controlled devices by establishing the EPICS IOC run-time databases. The user interface layer is developed by using Control System Studio to achieve transparent access to all controlled devices by operators. The machine protection system is designed based on safety rules to realize protection in the case of abnormal operations. It is used in the first underground ECR ion source in China and is stable and reliable, which fully meets the needs of the JUNA tuning and physical experiments.