We propose a new multiscale simulation method which seamlessly combines the conventional molecular dynamics (MD) with the continuum mechanics formulated under the material point method (MPM). In MPM, modified interpolation shape functions are adopted to reduce artificial forces on the hierarchical background grids. The multiscale method is validated using the examples of step-like wave and wave packet propagations within a bar. The method is applicable to several kinds of potentials including the Lennard–Jones, EAM and a bonding-angle related potential for silicon. Examples of high energy Cu–Cu and Si–Si cluster impacts are presented. The evolution of displaced atoms is found to depend on the underlying lattice structures. For the case of Cu–Cu cluster impacts, stacking faults play an important role. The displaced atoms, visualized in the method of “local crystalline order”, propagate in an anisotropic manner. This implies the anisotropy in energy transformation process through multi-interactions among cluster and surface atoms.