Abstract: In order to improve the consistency of Flash switch cell in Flash based FPGA after erasing and programming, a step method of erasing and programming Flash cell was designed. This method is used to perform several configuration operations on the Flash switch cell successively. After one configuration operation, the Flash current reading circuit reads back the Flash switch cell current, and adjusts the parameters of the next configuration operation based on the current reading back until the configuration operation is complete. By adjusting the operating voltage and time parameters during programming and erasure, the step control algorithm can accurately control the threshold voltage distribution of Flash switch cell after erasure and programming, ensuring the consistency of driver, and providing high precision delay parameters for Flash based FPGA. And the step configuration method is used to control the occurrence of Flash cell over-erasing and over-programming, so that the current reading circuit can accurately read the current of the Flash cell. The experimental results show that the threshold voltage of the erased and programmed Flash cell can be controlled within a preset range by using this step configuration method.