Three types of pure geopolymer pastes (poly-sialate PS, poly-sialate-siloxo PSS, and poly-sialate-siloxo PSDS) were first prepared by alkali (NaOH and KOH) activated metakaolin. Then a void space network was employed to simulate the 3-D pore-throat distribution across the unit cell of the various hardened geopolymer pastes with reference to their experimental mercury intrusion curves. Based on the simulated 3-D pore-throat structure models, a wide range of pore-level properties such as porosity, connectivity, permeability and tortuosity of various geopolymer pastes were calculated. The 3-D structural model and calculated parameters showed that most of the pores in Na-PS geopolymer paste was very small size pores ranging from 0 to 100 nm. A few very large pores were spread amongst the small pores, resulting in a very high penetration pressure, permeability resistance. Unlike Na-PS geopolymer paste, pore size with medium size of Na-PSS, K-PS and K-PSS geopolymer pastes distributed uniformly across the unit cell, and the size changes of adjacent pores in the 3 geopolymer pastes were little, producing higher penetration pressure, lower permeability, smaller connectivity and larger tortuosity. In contrast, pores in Na-PSDS and K-PSDS geopolymer pastes were relatively large and distributed concentratively, which caused samples to be easily penetrated by mercury, methane and nitrogen etc under relatively low pressures.