In wireless implantable neural signal acquisition system, the transmitting of the configuration data to the internal module needs high reliability. Therefore, differential coding is often used in this data transmitting system. However, it requires highly reliable clock synchronization between the internal and external system, leading to the design extremely difficult. To solve this problem, a new data encoding method based on pulse width modulation is presented in this paper to make the internal and external modules can work at asynchronous system clocks with a clock detector designed to make the internal device fit the different clock frequencies. The new coding method is shown to be successful by a board circuit system and the testing results.