In order to solve the problems of upgrading inconvenience in some DSP embedded systems, this paper proposes a method of onchip Flash programming based on serial communication. This paper describes the basic idea and implementation steps of the online programming methods. Considering the needs of practical projects, it optimizes the timing of receiving upgrade instructions and allocates application backup area in the onchip Flash. With these steps, the reliability and security of the system are improved. Besides, the system′s fault tolerance and selfhealing ability are enhanced. Experiment results show that the method is effective, simple and reliable. Compared with traditional programming method based on JTAG, it can be operated off the simulator, which improves the maintainability of the embedded system.