We demonstrate a novel method to characterize structural irregularities in a highly birefringent photonic crystal fiber (HB PCF) with high accuracy based on polarization coupling by torsional acoustic wave. Birefringence variation induced by the irregularities of air-hole structure in the fiber cross-section is analyzed via the transmission spectra of the acousto-optic coupling between two orthogonal polarization modes propagating along the fiber. The estimated maximum birefringence variation of two sections in the same batch of the HB PCF is 3 x 10-6 and 10-5, respectively, from nominal birefringence value of 4.86 x 10-4). The comparison between the experimental results and the numerical simulation resulted in the estimation of few tens of nm variation in the air-hole structure in the PCF.