The invention relates to a method for high efficiently debugging by using software breakpoint in a Flash memory. A Flash software breakpoint management controller, a Flash procedure downloader and an instruction resolver are arranged in a debugger; the debugger is connected to a target processing system through an ICE (internet communications engine); the debugger is used for controlling the target processing through the ICE, acquiring and modifying the state of a processor, and reading the data of the Flash memory; and the Flash software breakpoint management controller is used for storing and managing the Flash software breakpoint information, controlling the Flash software breakpoint state transition, controlling the operations of creating, deleting, recovering, shielding, enabling and updating the Flash software breakpoint, and controlling the implement of exchanging instruction sets. By using the method for high efficiently debugging by using software breakpoint in a Flash memory, the debugging time is shortened by reducing the Flash erasing operation; especially, the proceeding running from the Flash software breakpoint is as quick as the operation of arranging the software breakpoint in a RAM (random-access memory); the service life is influenced by the Flash erasing operation, thereby being capable of efficiently increasing the service life of Flash by reducing the Flash erasing operation.