A control device having a graphical user interface for controlling the operation of a transport refrigeration unit is disclosed. The graphical user interface may include a menu structure having multiple levels of menu options, executable functions and data items that may be navigated and viewed by a user. Access to the various menus may be user-specific and controlled so that a subset of the information in the menu structure is available to normal users, and larger subsets of the information are available to advanced users having higher levels of authorization to the menus and information contained in the graphical user interface device. The graphical user interface may also include programmable soft keys that may take users directly to frequently viewed menu options, functions and data items without the necessity of navigating through the levels of the menu structure.