The invention relates to a variable-depth cable ghost wave suppression method based on wave equation boundary value inversion. The method includes the following steps: 1) extracting a common-shot-point gather from seismic data collected by a variable-depth cable; 2) performing one-dimensional Fourier transform on the seismic data of a certain shot of the common-shot-point gather to obtain a frequency spectrum containing ghost wave seismic data; 3) calculating frequency domain seismic data U containing ghost waves corresponding to a certain frequency omega in the frequency spectrum; 4) calculating G1 and G2 according to detection point depth H<0><(2)>; 5) calculating frequency domain seismic data F after ghost wave suppression which are corresponding to the frequency omega according to U, G1 and G2; 6) performing steps 3) to 5) on all frequencies omega on the frequency spectrum in the common-shot-point gather to obtain frequency domain seismic data after ghost wave suppression; 7) performing steps 2) to 6) on other shots in the common-shot-point gather to obtain frequency domain seismic data after ghost wave suppression; and 8) performing inverse Fourier transform on frequency domain seismic data F after ghost wave suppression to obtain a common-shot-point gather after ghost wave suppression. The variable-depth cable ghost wave suppression method based on wave equation boundary value inversion can be used in the processing process of seismic data collected by a maritime variable-depth cable.