The present invention relates to an MFA (Metabolic Flux Analysis) information system using an XML (eXtensible Markup Language) and an operating method thereof. More specifically, the invention relates to an MFA information system and an operating method thereof, which generates, edits, stores and visualizes an MFA model feature and an MFA object using XML, and edits, stores and visualizes the result obtained by performing MFA based on the object. The present invention provides the MFA information system and method capable of generating, editing, storing and visualizing MFA model features and MFA objects using XML. Accordingly, MFA can be easily performed by utilizing advantages of XML, such as transplantation, reusability, deciphering, scalability, flexibility and effective data exchange, and thus the present invention can be applied to cell improvement using metabolic engineering.