From integrated optical circuits to long-haul fiber-optic networks, most photonic devices and communication systems rely on low-loss optical fibers. One of the key parameters affecting the transmission performance of optical fibers is their refractive index distribution, which determines characteristics such as insertion loss, propagation modes, and bandwidth of optical fibers. However, internal defects within the fiber can cause scattering or absorption of the optical signal during transmission, leading to attenuation and leakage of the output optical signal. Therefore, accurately and rapidly measuring the refractive index distribution and internal defects of optical fibers is of great significance for the optimization of fiber structure design and quality monitoring. Currently, the main methods for measuring the refractive index of optical fibers include the refractive near-field method, atomic force etching method, focusing method, thin-film interferometry, and transverse interferometry. Among these, transverse interferometry based on microscopic imaging requires no pre-treatment of the fiber. The fiber can be directly immersed in a matching liquid to achieve rapid, non-destructive measurement of the three-dimensional refractive index of the fiber. Therefore, this paper aims to construct a transverse interferometric system to reconstruct the three-dimensional refractive index distribution of optical fibers, enabling the detection of internal geometric structures and defects within the fiber. Based on the method of microscopic interferometry, this paper designs a cylindrical lens system for fiber measurement that effectively compensates for imaging astigmatism and proposes a high-precision transmissive transverse microscopic interferometric tomography system and method based on the cylindrical lens. First, a fiber simulation model was established based on the Finite Difference Time Domain (FDTD) theory for simulation verification. The results showed that the refractive index reconstruction error was extremely small, verifying the feasibility of the measurement method. Secondly, regarding the selection of the refractive index matching liquid in the experiment, the refractive index distribution of the fiber was reconstructed through single-direction projection to determine the optimal refractive index difference between the matching liquid and the fiber cladding. On this basis, three-dimensional refractive index tomographic reconstruction experiments were conducted on both multimode and single-mode fibers, and the results were compared with those obtained using a spherical lens. The results showed that the measurement error of the fiber core diameter using the cylindrical lens system was reduced by a factor of 10, and all measured values were within the given error range. Furthermore, the fiber defect detection experiment results indicated that the size, shape, and location of internal fiber defects could be identified through the reconstruction of the three-dimensional refractive index distribution of the fiber.