In this paper, the weighted class fractional Fourier transform is redefined by means of the weighted superposition of state functions, and the Fourier transform is applied to dissect the intrinsic relationship between the M-WFRFT and the 4-WFRFT and to obtain the weighting coefficients of the electronic communication signals. On the basis of the WFRFT discrete algorithm, the electronic communication signal is expanded to include M a term after the M -WFRFT and the hybrid carrier modulation method based on the WFRFT is given. According to the design idea of the electronic communication system, the hardware part and software part of the electronic communication system are designed, and the electronic communication signal modulation recognition system is experimentally analyzed by using the simulation experiment method. The results show that when the signal-to-noise ratio is -8dB and the optimization algorithms are the Sgd algorithm, Sgdm algorithm, and Adam algorithm, the modulation identification accuracy of OFDM signal is 39.3%, 57.5% and 43.5%, respectively, which indicates that the Sgdm optimization algorithm is the most suitable one compared with other algorithms, and it is more effective in the modulation identification of OFDM signals at low signal-to-noise ratio. The number of scans of the three-layer multi-parameter WFRFT signal by the non-cooperative party is 6.4 × 1013 times, and the increase in the number of scans leads to an increase in the cost paid by the non-cooperative party, which confirms that the secure communication system based on three-layer weighted fractional-order Fourier transform has good resistance to parameter scanning characteristics and high confidentiality. This study further improves the a priori parameter setting of the electronic communication system and enhances its complexity, resulting in better anti-interception identification features.