The invention relates to a method used for compensating the polarization mode dispersion in a wavelength division multiplexing system; the method multiplexes optical signals with different wavelengths of an optical fiber communication line into a channel; the polarization mode dispersion output by an optical multiplexer and transmitted through a certain distance of optical fiber link is compensated by a compensator; the compensated optical signals are de-multiplexed to the original optical signals with different wavelengths; a computing control device calculates and compares the polarization degree value of each path respectively, and chooses the channel with the worst polarization degree value to perform the worst channel compensation; the computing control device adopts a control algorithm to control the compensator to perform the compensation again, therefore, when the worst channel is compensated, the performance of other channels is guaranteed. The method has the advantages that the method can dynamically, effectively, rapidly and real-timely compensate the polarization mode dispersion of various channels in the wavelength division multiplexing system (WDM); the worst channelis compensated, therefore, the performance of the worst channel is the best; only one compensator is used for simultaneously compensating all the channels; when the worst channel is compensated, the performance of other channels is guaranteed, thus greatly saving the cost.