As a low-carbon, environment-friendly and economical resource for nuclear power generation, radionuclide emission and storage has received worldwide attention. Geopolymer concrete is a green and sustainable building material that can be used to immobilize radionuclides. In the present study, molecular dynamics simulations were conducted to investigate the structural and mechanical properties of sodium aluminosilicate hydrate (NASH) gel, the main component of geopolymer concrete, with/without immobilized radioactive Cs and Sr ions. The three-dimensional structure of NASH gel enabled good immobilization of both radioactive Cs and Sr ions owing to the large radius of Cs ions and high charge density of Sr ions. Addition of Cs ions reduced the strength of the gel and increased the fracture strain, whereas addition of Sr ions increased the strength and significantly increased the ductility. Addition of Sr ions increased the number of penta-coordinated Al in the structure. Consequently, breakage of these bonds required more energy to be absorbed from outside. The nanoscale molecular dynamics simulations provided a theoretical support at atomic level for understanding the structural and mechanical characteristics of geopolymers pertinent to the immobilization of nuclear waste.