An air handling unit control system is applied to an air handling unit having a plurality of hardware devices. The air handling unit control system includes at least one expansion module and a main controller. The at least one expansion module is configured to be electrically connected to at least one expanded hardware device. The main controller is electrically connected to the expansion module to control the expanded hardware device. The main controller provides a setting interface according to the hardware devices and the expanded hardware device. The setting interface includes a plurality of setting items. When at least one of the setting items is triggered, the main controller executes a corresponding setting procedure according to the triggered setting item to set up the hardware devices and the expanded hardware device.