ing at the problem of multiple and overlapping faculae of the birefringence sun sensor, a high-precision facula center extraction method based on ellipse fitting is proposed. After preprocessing for multiple facula images, different regions of interest are segmented. Then, the overlapping faculae are quickly distinguished and segmented by detecting the shape features of facula in the regions of interest. Finally, the central coordinates of each facula are extracted by ellipse fitting method. The simulation results show that the method can quickly distinguish overlapping faculae, calculate the number and radius of faculae, and extract the sub-pixel central coordinates of the circular and ellipse faculae. This method has no limitation on the size and quantity of faculae, and it can get satisfactory results for incomplete faculae.