Because of the inherent quasibrittleness and heterogeneity, matrix-directed toughening of concrete and cement composites remains to be a huge challenge. Herein, inspired by nacre materials, a novel biomimetic bulk cement composite is fabricated via a facile and efficient process based on compacting prefabricated multisized cement-polymer hybrid prills. This method combines with the three-dimensional "brick-bridge-mortar" structure design and synchronously the intrinsic and extrinsic toughening strategies. Such an approach shows the remarkable maximum toughness enhancement of 27-fold with 71% increase in flexural strength via cooperation with only 4 wt % organic matter. More attractively, it alters the traditional brittle fracture of cement composites to a distinct ductile fracture. In addition, such a biomimetic composite demonstrates the long-term ever-increasing strength and toughness, performing the excellent ductile-fracture retention ability. The hierarchical toughening mechanisms are further revealed with the synergy of microscopic characterizations and simulation methods. This strategy provides a new route for the development of high toughness biomimetic cement-based materials for potential applications in civil engineering domain.