Abstract: Aiming at the shortcomings of the traditional amplitude spectrum of the transform domain communication system used by binary coding method, which does not make full use of the jamming spectrum information and single structural design, a novel optimal bit error rate multiple amplitude spectrum coding algorithm is proposed. The algorithm derives the dynamic relationship among the bit error rate, amplitude spectrum and jamming spectrum information of the communication system of the transform domain, and transforms the amplitude spectrum coding into the constrained multidimensional optimization problem. Then the augmented objective function is constructed by using the Lagrange function, and the multiple amplitude spectrum optimal solution is solved through iteration. The simulation results show that the multiple amplitude spectrum coding algorithm takes full account of the jamming spectrum information and does not affect the correlation characteristics of the base function. Comparing with the traditional binary amplitude spectrum coding algorithm, it gets the jamming tolerance gain about 3dB. It can effectively alleviates the flat bottom phenomenon of bit error rate when jamming to signal ratio is 35dB . The anti- jamming of the system is improved.