Microcapsule based self-healing concrete can automatically repair damage and improve the durability of concrete structures, the performance of which depends on the binding behavior between the microcapsule wall and cement matrix. However, conventional experimental methods could not provide detailed information on a microscopic level. In this paper, through molecular dynamics simulation, three composite models of Tobermorite (Tobermorite 9 Å, Tobermorite 11 Å, Tobermorite 14 Å), a mineral similar to Calcium-Silicate–Hydrate (C–S–H) gel, with the linear urea–formaldehyde (UF), the shell of the microcapsule, were established to investigate the mechanical properties and interface binding behaviour of the Tobermorite/UF composite. The results showed that the Young’s modulus, shear modulus and bulk modulus of Tobermorite/UF were lower than that of ‘pure’ Tobermorite, whereas the tensile strength and failure strain of Tobermorite/UF were higher than that of ‘pure’ Tobermorite. Moreover, through radial distribution function (RDF) analysis, the connection between Tobermorite and UF found a strong interaction between Ca, N, and O, whereas Si from Tobermorite and N from UF did not contribute to the interface binding strength. Finally, high binding energy between the Tobermorite and UF was observed. The research results should provide insights into the interface behavior between the microcapsule wall and the cement matrix.