Abstract: Many existing fiber optic refractive index measurement systems are aimed at axisymmetric fibers, in this article, according to the characteristic of non-axisymmetric optical fiber, the optical path system is built by using digital holographic microscopy, based on the phase information of the measured sample carried by the object light wave, the information of the object light wave on the CCD is extracted, the phase distribution information of each hologram is extracted by the reconstruction algorithm of angular spectrum theory, and the three-dimensional refractive index distribution is obtained by the reconstruction algorithm of tomography. Then, using Changying Tong and Corning fibers as test samples, the difference in refractive indices between the fiber core and cladding is measured to be 0.005 and 0.006, respectively, which is basically consistent with the parameters provided by the manufacturer. In order to further verify the effectiveness of the testing method proposed in this article, refractive index measurements were conducted at the solder joints. The experimental results showed that the accuracy of the proposed measurement method is superior to previous fiber optic measurement methods, and it has advantages such as non-destructive testing of fiber optic samples, simple measurement methods, and fast measurement speed.