Geopolymers can be classified as an emerging, environmentally-friendly construction material. The dense structure of geopolymers means that they are effective for the immobilization of radioactive ions. However, the mechanical properties are intricately affected by radioactive ions, pore size and initial crack, and the underlying mechanisms require further investigation. This study employs a combined molecular dynamics (MD) and peridynamics (PD) approach to analyze the effects of radioactive ions and how changes in pore size and the presence of an initial crack influence the mechanical performance of geopolymers. The results reveal that Cs and Sr ions exert opposing effects on the mechanical properties of NASH; more specifically, Cs ions negatively affect the mechanical properties of geopolymers. Pore size demonstrates a non-linear influence on performance, with models featuring pore diameters of 40–60 nm exhibiting the poorest mechanical properties. Moreover, the presence of an initial crack in the modeled geopolymer significantly reduces Young’s modulus and the ultimate tensile strength of the material. In the applied cross-scale approach, PD simulations validated and extended the MD results to align more closely with experimental values. This study provides a foundation through which multi-scale modeling can be leveraged to optimize geopolymer performance, particularly in the fields of nuclear waste immobilization and advanced construction materials.