Conventional building materials have been faced with significant challenges, including large carbon emissions, high density, and quasi-brittleness. Inspired from the hierarchical porous structure in nature, a low-carbon, lightweight, strong and tough cement-based material (LLST) was developed through in situ self-assembly strategy, which was accomplished by a rapid gelation of hydrogel as skeleton and subsequent deposition of cement hydrates as skin in order. As a results, the LLST exhibited hierarchical structure made up of sponge-like micropores (1 ~ 50 µm) and nanopores (5 ~ 100 nm), without detrimental macropores that compromise lightweight, strength, and toughness coordination. Compared with the normal cement paste, LLST displayed a 54% reduction in density, 145% and 1460% improvement in specific compressive strength and fracture energy, with only 36% carbon emission, which has not been realized in literature. Furthermore, such significant advancements were in depth revealed by ab initio metadynamics simulations, indicating that strong interactions, including van der Waals forces, hydrogen bonding and steric hindrance effects at atomic level, were generated between functional groups in hydrogels and Ca ion released from cement hydration. These findings not only bring a novel strategy for developing lightweight building materials with low-carbon emission and remarkable mechanical properties, but also provide valuable insights to realize the coordination of lightweight, strength and toughness by tailoring the hierarchical pore structure.