In order to solve the adaptive problem of generating jamming waveforms in response to enemy communication signals in Unmanned Aerial Vehicle(UAV) swarm communication confrontation, a cognitive jamming waveform design method is proposed based on Spectrally Modulated Spectrally Encoded(SMSE) model. By deploying six kinds of different waveform design parameters in the SMSE framework, the waveforms with a specific spectrum structure are synthesized in the frequency domain to generate cognitive jamming waveforms with corresponding functions to deal with communication signals under different parameters in communication countermeasures. Simulation experiments show that the theoretical model can generate the suppressive jamming waveforms: single-tone jamming, multi-tone jamming, wideband interference, and narrowband interference. It can also achieve modulation deceptive jamming for the modulation methods of BPSK, QPSK, 8PSK, and 16QAM signals. Compared with the theoretical curve, the experimental results verify the theoretical feasibility of SMSE model to generate cognitive interference waveform. SMSE model can realize the integration of suppressive jamming and spoofing jamming.