This study presents a five-phase mesoscale modeling framework specifically developed to investigate crack propagation and mechanical properties of biochar–cement composites. The multi-phase model includes porous biochar particles with precise geometric construction, sand aggregates, cement matrix, and interfacial transition zone adjunct to both the biochar particles and sand aggregates. The 3D porous biochar library was first proposed and established in this study, which could provide an external interface for describing different pore shapes, wall thicknesses, and pore areas. All the simulation results were experimentally validated using a digital image correlation. Through precise geometric modeling, the unique failure modes and timing of biochar particles within the mortar were identified. This is analogous to the “strong column–weak beam” concept, accounting for the enhanced ductility observed in the biochar–cement composites under compression test. This work can advance the geometric modeling of porous aggregates broadly and elucidate their mesoscopic failure mechanisms in cementitious materials, thus providing new insights for developing high-ductility and lightweight cement composites.