The invention discloses a program compiling method, device and system, and the method comprises the steps: obtaining a to-be-compiled program code which comprises a calling address of at least one stub function; obtaining an editing script of the program code, wherein the editing script is related to a calling address of the stub function; reconstructing a calling address of a target function, which is replaced by the calling address of the stub function, in the program code by utilizing the editing script and the calling address of the stub function; and compiling the program code based on the calling address of the objective function to obtain an executable file of the program code. Even if the executable file is disassembled, the content of the program code cannot be interpreted by theoutside due to the fact that the stub function exists in the disassembled program code, so that the purpose of protecting the program code is achieved, and the safety of the program code is improved.