To enhance the combat survival ability of secondary radar， the application of frequency diverse array in secondary radar is proposed， making use of the distance-angle-time coupling characteristics of frequency diverse array. The method of digital baseband composite frequency offset is used to reduce the implementation cost and complexity of FDA； optimize the beam sidelobe through differential logarithmic frequency offset to achieve the irradiation of dot-shaped beam at specific positions， improving the covertness and security of signal transmission； and propose the optimization design method of long dwell beam based on time-varying weighting to ensure the effective reception and recognition probability of secondary radar signals. The application research of FDA in identifying secondary radar lays the foundation for the development of new equipment and also provides reference for other system applications.