The invention relates to a hidden communication method based on transform domain processing, which comprises hidden communication sending end design and receiving end design. Firstly, a sending end carries out spectrum sensing on a channel environment, generates a spectrum matrix, carries out pseudo random phase modulation, generates a time-domain basis function by IFFT and normalization processing so as to implement spectrum aggregation, carries out a cyclic shift operation by using the time-domain basis function as a prototype, completes modulation processing of CCSK on transmission data, and forms a transmission signal; and a receiving end generates a local related sequence by spectrum sensing, obtains a local time-domain basis function by IFFT, carries out the cyclic shift operation, makes cross-correlation with the received signal, implements CCSK demodulation, and recovers original sent data. According to the invention, a complex electromagnetic environment an be promptly and adaptively sensed, a high hidden communication system is adopted, and hidden communication exists, so that uninterrupted information transmission is always kept, high confidentiality of data is ensured,and enemy reconnaissance and interference threats are effectively resisted to.