Understanding the pipeline scour mechanism under different conditions is essential for protection measures. The computational fluid dynamics (CFD) and discrete element method (DEM) are coupled for the simulations. To reduce the computational effort, the coarse-grained method is applied, and the Darcy-Forchheimer porous model is used to replace the far field elements. Both of the porous medium and particles-fluid interaction model are validated by comparison between simulation results and theories. The scouring simulation results show a good agreement with the experiments conducted with single-diameter spherical particles under different current-wave conditions. Further, the flow around the pipeline, the seepage in the sediment bed and the force acting on the particles are analyzed. The vortex shedding exists downstream under current but the vortex moves around under waves. The seepage depends on the pressure, influenced by the pipeline and the water depth, and the variation of the seepage is discussed. The force acting on the particles is not uniform along bed and the distribution is analyzed.This paper provides an insight into scour mechanics from the aspects including seepage and flow-particle interaction. Different methods are used for modification, giving a reference for the usage of CFD-DEM model in the analysis of scour process.