Many particle-based numerical models have been used to simulate the hydration process of cementitious materials. Most of those models employ regular shape particles, like the commonly used spheres, to represent cement, slag, or fly ash, which neglects the influence of particle shape. To deal with this issue, this study extended the Anm material model and used irregular shape particles to simulate the initial particle parking structures of cement/geopolymer pastes. The irregular shapes of cement, slag and fly ash particles were characterized by spherical harmonic series. Compared to the initial particle structures simulated using spherical particles, those using irregular shape particles had total surface areas and bulk specific surface areas with up to 37.40% and 36.84% larger, respectively. However, the pore size distributions of the simulated initial particle structures did not show significant influence of particle shape. As a demonstration to illustrate the influence of particle shape on dissolution, the initial particle parking structure of amorphous silica in alkaline solution was generated using irregular shape particles, and was used as input to simulate the dissolution of silica particles. The Lattice Boltzmann method was used to simulate the transport process of aqueous ions and thermodynamics was employed to consider the rate of dissolution of silica. The dissolved fractions of silica at different temperatures in the simulations agreed well with experimental measurements. The influences of continuous stirring, concentration of alkali and particle shape on the dissolution kinetics of silica were investigated numerically.