The invention discloses a medical nuclear magnetic resonance water chilling unit control system. The system comprises a control system and an electric cabinet. The control system comprises a manual operator and a control module. The control module comprises an unit initialization module, a water supply temperature, a flow control module, an alarm module, a historical record removing module, a data check module, a factory setting module and a controller. The control system is connected to the electric cabinet. The control module is connected to the manual operator. By using the medical nuclear magnetic resonance water chilling unit control system, the manual operator and the control module are connected so that working personnel can conveniently operate; Simultaneously, through setting each function module in the control module, an operation condition of a water chilling unit can be timely monitored and managed; the data can be well stored and managed and practicality of the water chilling unit is increased so that complete functions are possessed and a cooling effect is effectively guaranteed.