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In this work, a multiscale cohesive zone model (MCZM) is developed to simulate the high-speed penetration induced dynamic fracture process such as fragmentation in crystalline solids. This model describes bulk material as a local quasi-continuum medium which follows the Cauchy–Born rule while cohesive zone element is governed by an interface depletion potential, such that the cohesive zone constitutive descriptions are genetically consistent with that of bulk element. This multiscale method proved to be effective in describing material inhomogeneities and it is constructed and implemented in a cohesive finite element Galerkin weak formulation. Numerical simulations of high-speed penetration with different shape of penetrators, i.e., square, circle and parabola nose penetrators are performed. Results show that the proposed MCZM can successfully capture spall fracture, the penetration process and different characteristics of fragmentation under different shape of penetrators.