The present disclosure discloses a method for customizing a desktop launcher of a mobile terminal, comprising: placing a resource file and a configuration file for customizing at least two kinds of desktop launchers in a resource folder and a configuration folder, respectively, wherein the files and the folders of the desktop launchers are different in name; adding a compilation command corresponding to the at least two kinds of desktop launchers, and copying the resource file and the configuration file corresponding to the at least two kinds of desktop launchers in a saving path to a second file directory; adding the saving path of the files corresponding to the at least two kinds of desktop launchers in the second file directory to a program information file; compiling the files in the folders corresponding to the desktop launchers in the second file directory, so as to generate an installation program APK file; and loading the installation program file corresponding to the desktop launcher selected by the user, so as to execute the corresponding desktop launcher. The present disclosure further provides a system for customizing a desktop launcher of a mobile terminal.