This paper investigates the mechanism of submarine pipeline penetration into calcareous sand by using centrifuge testing and discrete element modeling. The results indicate that the pipeline penetration resistance shows a linearly increase trend with the pipeline embedment, and its value is approximately equal to the product of pipeline-soil contact width and the cone penetration resistance obtained from the cone penetration test (CPT). When the pipeline embedment is small, the penetration resistance is almost unaffected by particle strength due to the fact that the soil deformation is dominated by the particle rearrangement. When the pipeline embedment is large, the penetration resistance decreases with decreasing particle strength and increasing particle breakage. The mechanism of pipeline penetration into calcareous sand exhibits a typical punching shear failure. The soil deformation primarily occurs at the bottom of the pipeline, and the teardrop-shaped deformation region gradually shrinks with increasing particle breakage. The particle breakage develops radially away from the bottom of the pipeline, where most successive particle breakages tend to occur near the pipeline, while a few individual breakages are more common in regions far from the pipeline. The particle breakage results in the release of stress concentration at the bottom of the pipeline. The more the particles break, the more the stress releases, and the more obvious the resulting decrease of penetration resistance.