Boron carbide ceramics are potentially ideal candidates for lightweight bulletproof armor, but their use is currently limited by their low fracture toughness. Recent experimental results have shown that sintered samples with high twin densities exhibit high fracture toughness, but the toughening mechanism and associated crack propagation process of nanotwinned boron carbide at the atomic scale remain a mystery. Reported here are molecular dynamics simulations with a reactive force field potential to investigate how nanoscale twins affect the fracture toughness of boron carbide ceramics. The results show that the strength disparity on either side of a twin boundary is the fundamental reason for the toughening effect; the twin boundary impedes crack propagation only when the crack moves to a region of higher fracture strength. The fracture toughness of nanotwinned boron carbide is greatly affected by the angle between the twin boundary and the prefabricated crack. At an angle of 120°, the twin boundary provides the maximum toughening effect, enhancing the toughness by 32.72%. Moreover, phase boundaries—another common structure in boron carbide ceramics—have no toughening effect. This study provides new insights into the design of boron carbide ceramics with high fracture toughness.