A 3D reactive transport model at microscale is proposed for simulating the chemical reaction process of alkali silica reaction (ASR) thermodynamically and kinetically including the dissolution of reactive silica, the nucleation and growth of ASR products and the dissolution of calcium hydroxide (CH) and calcium silicate hydrate (C-S-H) as a buffer of Ca2+ and OH− to ASR. The implementation methodologies are firstly explained. Sensitivity analyses are done to calibrate some important parameters. The model is then applied to investigate the influence of the silica microstructural disorder degree on ASR. The simulation results show that the model is able to simulate successfully two typical patterns of the expansion sites location depending on the silica reactivity (inside the aggregate or in the aggregate-cement paste zone) found in field concrete and laboratory samples. A possible mechanism is provided based on the quantitative data captured by the model. The model can be extended to a multiscale ASR model for physic-chemical simulation to bridge the gap between the fundamental chemical mechanisms and the physical response of concrete.