Hydraulic structures such as embankments and dams are essential for water storages, flood control, and transportation, but are vulnerable to suffusion under complex loading conditions. This study investigates the effect of suffusion on the cyclic shear behavior of gap-graded soils using the coupled computational fluid dynamics and discrete element method (CFD-DEM). A series of seepage infiltration and drained cyclic shear tests are conducted on specimens with varying mean stresses and initial stress anisotropy to systematically evaluate the mechanical consequences of suffusion. The findings reveal that the higher mean stress and initial stress anisotropy significantly exacerbate fines loss and deformation, particularly along principal seepage directions during suffusion. Furthermore, the eroded specimens exhibit substantial stiffness degradation and microstructural changes, including the deteriorated interparticle contacts and more pronounced fabric anisotropy. Notably, fines loss intensifies the load-bearing reliance on coarse particles during cyclic loading. These results provide new micromechanical insights into suffusion-induced degradation, offering valuable implications for developing advanced constitutive model of gap-graded soils accounting for suffusion-induced fines loss and cyclic loading conditions.