A critical obstacle to the design of more sustainable and durable cement-based material is its relatively low flexural strength and susceptibility to brittle fracture. In this paper, a novel cement-polymer composite was developed by in-situ crosslinking polymerization of sodium acrylate monomers and the synchronous hydration of ordinary Portland cement. In-situ polymerization in cement paste can significantly shorten the initial setting time to less than 10 min and the cement hydration process is inhibited during ions dissolution and dynamic balance stage. In-situ polymerization produces the intertwined inorganic-organic network, bridging the defections of cement paste at micro-level. Due to the formation of double-network structure, as compared with OPC, the optimized design can obtain 15% improvement in compressive strength and 200% improvement in flexural strength. The monomer to cement ratio and initiator to monomer ratio are essential factors for improving mechanical properties of composites. Furthermore, molecular dynamics is utilized to investigate the structure, dynamics and mechanical properties of interfacial bonds between sodium polyacrylate molecule and cement hydrate. The carboxyl groups in the polyacrylate provides oxygen sites to accept H-bond from protonated silicate tetrahedron and neighboring water molecules. The calcium and sodium ions play bridging role in connecting oxygen atoms in functional group and oxygen in silicate chain of calcium silicate hydrate. The H-bond, O–Ca–O and O–Na–O salt bridges strengthen the interfacial bonding, which inhibits the cracking development and enhance the ductility of cement-polymer composite. Hopefully, this in-situ polymerization strategy can provide valuable insights on high-performance cement-based composite design.