Abstract Nowadays, geopolymers are advanced alternatives to cementitious materials, where their excellent chemical and fire resistance are some of its most appealing properties. Fly ash geopolymers enable the use of industrial waste materials while converting them into a novel binding material. Their production is accompanied by a much lower CO 2 emission when compared to Portland cement. Reinforcing fly ash geopolymers with carbon nanotubes would significantly strengthen its microstructure and with this enhancing the long‐term mechanical and durability performance. The aim of this work is to use reactive molecular dynamics simulation method to optimize the mechanical properties of fly ash geopolymers with nano‐reinforced carbon nanotubes (CNTs). During this study, the impact of humidity and interfacial bonding strength between carbon nanotube and geopolymer is investigated. Our findings show that structural transformations under hydration process comes from the weakening of AlO bond, leading to the elongation of AlO and NaOH bonds, forming aluminum and sodium hydroxyls. Conversely, silicate is not sensitive to water and exhibits hydrophobic behavior. In addition, our results show that there is an optimal value of water content (7.17 wt.%) that makes the geopolymer nanostructure strengthen. The related elastic modulus rises by 21.56%, 20.60%, and 18.41% for Si/Al ratio of 1, 2, and 3, respectively. Inserting carbon nanofillers to fly ash nanostructure has remarkably shown an interesting strength enhancement. More precisely, when interfacial bonding concentration is around 19.36%, it is observed a positively increasing of the compressive strength, shear, indentation and elastic modulus with 39%, 65.2%, 72.3%, and 144.85%, respectively. Reduced density gradient supports that the interaction between carbon nanotube and fly ash geopolymer is dominated by a van der Waals one.