The invention provides an automatic compiling method for graphical programming, which mainly comprises the following steps of allocating a graphical program memory, allocating a graphical program thread, analyzing a graphical program storage structure and generating a graphical program executable file. An executable file corresponding to a graphical program is generated based on automatic compiling of graphical programming, a user freely combines graphical modules according to functional requirements to form a program, an automatic compiling method for graphical programming is used for compiling the graphical program, and a file which can be directly operated in a controller is generated. An obscure executable file corresponding to the graphical program can be automatically generated without needing complicated compiler or compiling environment in the method, and then the generated executable file can be transmitted to the controller through data exchange for running, so as to achieve an action effect corresponding to the graphical program.