The flow direction is generally different from the gravity direction in geotechnical structures or slopes, the effect of which during suffusion remains unclear. This paper presents a coupled computational fluid dynamics and discrete element method approach to simulate the particle–fluid interaction relevant to this problem. The CFD-DEM approach is first benchmarked by a classic granular system problem, which is then used to investigate the characteristics of suffusion and its impact on the mechanical behavior. Five different angles between gravity and seepage directions for gap-graded soils with two fines contents are examined. Both the macroscopic and microscopic characteristics during suffusion and triaxial loading tests are analyzed. The direction angle is found to play a significant role affecting the erosion process and the mechanical consequence of soils. The results show that the greater the angle is, the harder it is for suffusion to occur and continue.