Abstract: In some kinds of Computer-based Interlocking System, secure coding was used for input and output to guarantee the safety of acquisition and driving. Secure coding should be programmed into the safety input/output board’s Flash memory previously. According to the state of security coding, the input/output board determined whether the system worked properly. The paper designed a programmer which used 80C51F020 single-chip microcomputer as its controller, and also designed the PC program based on Qt to implement the operation of 28F128J3F75 Nor Flash chip, including input / output board of automatic identification, read / write secure coding, etc. It was described the system architecture, hardware connections, software design and the data format definition of PC program reading or writing secure coding in detail.