According to the characteristics of non-axisymmetric optical fiber, the optical path system was built by using digital holographic microtomography. 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 was extracted. Due to the characteristics of non-axisymmetric optical fiber, a 360° digital hologram was collected. The phase distribution information of object light wave of each hologram was extracted by the reconstruction algorithm of angular spectrum theory, and the three-dimensional refractive index distribution was obtained by the reconstruction algorithm of tomography. Then, the Changying Tong and Corning fibers were used as test samples, the difference in refractive indices between the fiber core and cladding was measured to be 0.005 and 0.006, respectively, which was basically consistent with the parameters provided by the manufacturer. In order to further verify the effectiveness of the proposed testing method, the refractive index measurements were conducted at the solder joints. The experimental results show 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.