Disclosed herein are a method and apparatus for performing a configuration of an aeronautical system. The apparatus includes a display unit, an intermediate model generation unit, an Extensible Markup Language (XML) conversion unit, and a translator. The display unit display displays a user interface for receiving aeronautical system setting information in compliance with an ARINC 653 standard. The intermediate model generation unit generates an intermediate model of source code based on the setting information received via the user interface. The XML conversion unit creates an XML document by performing XML conversion on the generated intermediate model. The translator generates a source code file in compliance with the ARINC 653 standard by converting the generated XML document.