The invention provides a rapid frequency domain coding method for a quasi-cyclic multi-system low density parity check code. The method comprises: a step 1) of calculating a segment look-up table of Fourier transform and a segment look-up table of inverse Fourier transform; a step 2) of acquiring a generated matrix G of a system form, and performing rapid Fourier transform on the generated matrix G by using the segment look-up table of the Fourier transform to obtain a generated matrix of a frequency domain; a step 3) of transforming an input sequence u to the frequency domain by using the segment look-up table of the Fourier transform, and calculating a coding sequence of a redundant check part on the frequency domain according to the generated matrix of the frequency domain; and a step 4) of performing rapid Fourier inverse transform on the coding sequence of the redundant check part on the frequency domain by using the segment look-up table of the inverse Fourier transform to obtain a coding sequence of a redundant check part on a time domain. Through adoption of the method provided by the invention, the calculation amount and calculation complexity of the multi-system low density parity check code can be lowered greatly; the energy consumption demand on a hardware platform is lowered; and the requirements of application scenes such as underwater acoustic communication are met.