In this paper, an novel polarization maintaining fiber（PMF） alignment method based on fiber loop mirror（FLM）has been proposed and developed. The two PMFs to be spliced were fused to the two arms of a 3dB coupler and the other end faces of them were connected to build a FLM.The transmittance function of the FLM has been derived and the method to calculated the angle between the polarization axes of the two PMFs has been deduced. Finally, by analyzing the output spectrum of the FLM, the angle between the two PMFs can be calculated out and the two PMFs can be polarization aligned at any angle. The method has been analyzed in detail and verified by numerical simulation and experimental research. This method is applicable to all types of PMFs with high accuracy.