Despite the crucial role of concrete in the construction of nuclear power plants, the effects of radiation exposure (i.e., in the form of neutrons) on the calcium–silicate–hydrate (C–S–H, i.e., the glue of concrete) remain largely unknown. Using molecular dynamics simulations, we systematically investigate the effects of irradiation on the structure of C–S–H across a range of compositions. Expectedly, although C–S–H is more resistant to irradiation than typical crystalline silicates, such as quartz, we observe that radiation exposure affects C–S–H’s structural order, silicate mean chain length, and the amount of molecular water that is present in the atomic network. By topological analysis, we show that these “structural effects” arise from a self-organization of the atomic network of C–S–H upon irradiation. This topological self-organization is driven by the (initial) presence of atomic eigenstress in the C–S–H network and is facilitated by the presence of water in the network. Overall, we show that C–S–H exhibits an optimal resistance to radiation damage when its atomic network is isostatic (at Ca/Si = 1.5). Such an improved understanding of the response of C–S–H to irradiation can pave the way to the design of durable concrete for radiation applications.