Modeling the plastic deformation of crystalline materials by all atomistic methods remains a challenge, and large-scale methods, such as coarse-grained (CG) methods, are highly desirable. To overcome difficulty in constructing CG potentials for stiff molecular crystals by conventional approaches, we propose a limited sample coarse-grained (LSCG) strategy. We construct a CG potential of α-1,3,5-trinitro-1,3,5-triazinane (RDX), a widely used energetic material, and perform coarse-grained molecular dynamics (CGMD) simulations to validate the LSCG potential. We compare the calculated mechanical properties with other reported results. Results show that the LSCG method is effective when compared with the all atomic potentials and provides adequate insight into systems with larger scales. Therefore, through the LSCG method, the deformation mechanisms of α-RDX crystals under nanoindentation conditions are revealed by a series of CGMD simulations that resemble nanoindentation on its (100) surface with nano-holes sited differently. Valuable results are obtained and understood. That is, the stress around the nano-hole can trigger void collapses when the nano-hole is located at a shallow position directly beneath the indentation surface. At a location deeper than four times of the maximum impression depth, the stress around the hole is extremely weak to cause the void collapse. Most of the dislocation loops are found to be parallel to the (001) plane, which is attributed to the low slip threshold of the (010) [100] slip system. This result shows that the LSCG strategy can deal with much larger systems and reveal mechanisms on the mesoscale.