With the rapid development of communication jamming technology, multi-channel jamming technology has attracted much attention. A method of multi-channel modulation by using Fourier matrix is proposed in order to produce multi-channel modulated jamming signal efficiently. Firstly, a two- dimensional square matrix is built, whose dimension depends on the system sampling rate and the duration of the signal. The elements of each line are determined by the signals to be modulated. The square matrix is multiplied by Fourier matrix, and the diagonal elements of the result form the multi-channel modulated signal. Compared with traditional method, the proposed one is simple, flexible and efficient for it is unnecessary to generate multiple-carrier to modulate the corresponding signals. In addition, a practical system is set up based on the communication jamming system, to perform the principle simulation and the practical performance tests. The results show that the method is feasible.