This paper aims to study the deflection of high-density polyethylene (HDPE) corrugated pipeline subjected to differential settlements of the ground using the finite difference method-discrete element method (FDM-DEM) coupling simulation method in 3D. Various physical characteristics of the pipeline, including diameters, corrugations, and elastic modulus have been investigated. Soil particles with different shapes are considered. The variation of soil settlement of soil particles with three different shapes under the uneven settlement condition is studied. The soil arching effects, including positive soil arch and negative soil arch, have been respectively analyzed. The results reveal that the change in pipe corrugation influences the stiffness of the pipe and the friction between the pipe and soil to some extent, which also causes the change of vertical deflection of the pipe. The soil composed of four particles is easier to form soil arch, which makes the soil more self-stabilized, thus alleviating the circumferential deformation of the pipeline.