For the problem of suffosion in gap-graded sand with initial anisotropy, the Ganser drag force model, which can take into account the effect of the projected area of particles, is introduced to achieve a two-phase coupling of computational fluid dynamics (CFD) and discrete elements method (DEM) for non-spherical particles. The applicability of the numerical method in solving the interaction between the non-spherical particles and fluid is verified by comparing with single particle settlement tests. On this basis, specimens with different bedding orientations and fine contents are further generated to simulate upward seepage suffosion tests, during which both macroscopic and microscopic properties, such as the fine loss, composition of strong and weak force chains, and changes in grain fabric, are monitored to explore the seepage suffosion characteristics of anisotropic soils with various fabrics under different filling states (underfilled and overfilled). Drained triaxial tests are carried out on specimens before and after erosion to investigate the effect of seepage on the weakening of soil strength. The results show that the mass loss of the overfilled specimens increases with increasing deposition angle, while the mass loss of the underfilled specimens firstly increases and then decreases with the deposition angle. The loss of fines in the underfilled specimens is mainly due to the low connectivity fines, whereas for the overfilled specimens, suffosion leads to a simultaneous reduction in the number of both low and high connectivity fines. In addition, the triaxial tests show that suffusion causes a significant weakening of the peak strength of the soil, and the change in peak strength with the deposition angle is also influenced by the soil filling state.