The aim of this paper is to develop a functional-based stack-up design system for stamping dies. By performing function analysis, function decomposition, and geometric analysis, design engineers are able to identify a particular die’s functional features and their main variables, which are used as the basic units for the stack-up design. This stack-up design system includes a die design knowledge base, a functional feature module, and graphic user interfaces. A functional-based stack-up design system has been implemented on a Windows operation system through interfacing Visual Basic codes with commercial software, CATIA and Automation API. To showcase the power of the system, an example of designing a lower of the drawing dies for roof outer panels is provided. Based on the experimental results, the system is an efficient, flexible and accurate stack-up system for designing die structures.