Embodiments of the present invention disclose an application protection method, a server, and a terminal. The application protection method includes: receiving an application download request that is for a target application and that is sent by a terminal, where the application download request carries terminal identification information of the terminal; compiling an application installation package of the target application according to the terminal identification information; and sending the compiled application installation package to the terminal, so that the terminal installs the target application in a running environment that is based on the terminal identification information, where the running environment is obtained by the terminal by compiling a preset intermediate file of the terminal according to the terminal identification information, and the preset intermediate file includes a runtime file and a framework file. In the embodiments of the present invention, application security can be effectively improved and stability of a software industry chain ecosystem can be effectively improved.