The invention relates to an intelligent heat exchange station controller and a control method thereof, belonging to the field of heat supply. The system comprises a central processing unit, an uninterruptible power supply, a power supply, a production control module, a production data acquisition module, a storage unit, a man-machine interaction module, a communication module and a short message sender. The uninterruptible power supply, the production control module, the production data acquisition module, the storage unit, the man-machine interaction module, the communication module and the short message sender are all connected with the central processing unit, and the power supply is connected with the uninterruptible power supply. The method can optimize the operation adjustment decision mode of the heat exchange station, can improve the automatic control level, can strengthen the alarm capability of emergency events, can improve the timeliness of accident handling, and can ensurethe personnel reduction and the efficiency improvement of the operation management of the central heating heat exchange station in winter.