Mechanisms governing the sand plug behavior inside an open-ended pile are examined using the discrete element method. A series of numerical pile penetration tests have been conducted by considering the influence of soil density, pile geometry and installation method. A novel sample generation method, based on the replication of unit cell, is applied to produce a large and homogeneous sample efficiently. According to the soil deformation pattern, a “nose cone”, with the length about one pile diameter, has been observed beneath the small diameter jacked pile at the end of penetration. Plugging effect is shown to be more prevalent for jacked piles than dynamic installed piles. Also, larger penetration, smaller diameter and higher soil density all seem to promote plug formation, while the influence of wall thickness is not that obvious. This conclusion is later verified by the development of Incremental Filling Ratio (IFR) and porosity distribution. Furthermore, remarkable stress concentration has been observed at the lower part of the soil plug. The development of installation resistance indicates that jacking produces the largest resistance while dynamic installation methods ease pile penetration. Further analysis based on particle movements, contact force chain distribution and stress orientation provides a micromechanical perspective of the plug behavior. Finally, the plug resistance mobilization process at different plugging conditions and the formation process for soil plug are illustrated.