The purpose of this study was to investigate the deformation behavior of non-spherical particles during high-load compaction using the multi-contact discrete element method (MC-DEM). To account for non-spherical particles, the bonded multi-sphere method (BMS), which incorporates intragranular bonds between particles, and the conventional multi-sphere (CMS), where overlaps between particles are allowed to form a rigid body, were used. Several test cases were performed to justify the conclusions of this study. The bonded multi-sphere method was first employed to study the compression of a single rubber sphere. This method’s ability to naturally handle large elastic deformations is demonstrated by its agreement with experimental data. This result was validated further through detailed finite element simulations (multiple particle finite element method (MPFEM)). Furthermore, the conventional multi-sphere (CMS) approach, in which overlaps between particles are allowed to form a rigid body, was used for the same objective, and revealed the limitations of this method in successfully capturing the compression behavior of a single rubber sphere. Finally, the uniaxial compaction of a microcrystalline cellulose-grade material, Avicel® PH 200 (FMC BioPolymer, Philadelphia, PA, USA), subjected to high confining conditions was studied using the BMS method. A series of simulation results was obtained with realistic non-spherical particles and compared with the experimental data. For a system composed of non-spherical particles, the multi-contact DEM showed very good agreement with experimental data.