This study presents an extended numerical approach based on GeoMicro3D to simulate the reaction kinetics and three-dimensional (3D) microstructure evolution of alkali-activated fly ash (AAFA). Dissolution experiments were conducted under varying NaOH concentrations and temperatures to formulate predictive rate functions for Si and Al release. These experimentally derived kinetic functions, alongside a thermodynamic dataset for N-(C-)A-S-H gels, were incorporated into the GeoMicro3D model to capture the chemical reactions and 3D microstructure evolution of AAFA. The model well captured reaction degree of fly ash, formation of solid products, evolution of pore solution compositions, and porosity over time. Notably, it is the first to predict the time-dependent spatial distribution of phases within the 3D AAFA microstructure by integrating kinetic and microstructural modeling. Dual validation using both dissolution data and microstructural metrics demonstrates the model's reliability and robustness. This integrated framework provides new insights into the coupled chemical–microstructural evolution of alkali-activated materials.