Photonic crystal fiber (PCF) has many special characteristics, which strongly depend on its structure. The location error or deformation of the cladding holes can be introduced readily during the complex fabrication process, which will change the characteristics of the PCF intensely. A commercial single-mode polarization-maintaining PCF was investigated when the size and location of one of the two larger side holes were changed. In order to give relationship between the location error or deformation of the cladding holes and the dispersion characteristics, the simulations of the PCF dispersion characteristic were given for the case that the location of one side larger hole was changed while the size and form kept invariable. Secondly the case, that the size of one side larger hole was changed without shifting, was simulated. The simulation results for the case of changing both location and size of this hole were demonstrated at last. All the simulation results show that the structure deformation affects the properties of the polarization-maintaining PCF strongly because the effective index of refraction, zero group velocity dispersion wavelength, polarization beating length, mode structure etc. are changed.