The invention discloses a method for customizing a linux operating system, wherein the customization refers to modifying the system according to the requirements of users so as to meet the requirements. The method provided by the invention mainly comprises the following steps of: parsing software packages in a software repository, classifying the software packages, analyzing the dependency relationship between the software packages and generating a software repository searching catalog, and providing the software repository searching catalog for the users in a Web manner for selection or searching the software packages; obtaining user configuration information, generating configuration files necessary for making Live CD (Compact Disc), Install CD and Live USB (Universal Serial Bus) according to the user configuration, then, automatically generating a corresponding customization system file by a server end program based on the working principle of the Live CD, the Install CD and the Live USB, and finally, writing the customization system file in storage media, such as a CD or a DVD (Digital Video Disk), a USB flash disk and the like. The method provided by the invention can implement the automatic customization and mass production of the operating system, largely.