Sintered agglomerate of synthetic mesoporous silica nanoparticles (MSNs) is an architected geomaterial that provides confinement-mediated flow and transport properties of fluids needed for environmental research such as geological subsurface energy storage or carbon capture. The design of those properties can be guided by numerical simulations but is hindered by the lack of method to characterize the permeable pores within MSNs due to pore size. This work uses the advances of an Individual Particle cryogenic transmission Electron Tomography (IPET) technique to obtain detailed 3D morphology of monodispersed MSNs with diameters below 50 nm. The 3D reconstructed density-maps show the diameters of those MSNs vary from 35–46 nm, containing connected intraparticle pores in diameter of 2–20 nm with a mean of 9.2 ± 3 nm, which is comparable to the mean interparticle pore diameters in sintered agglomerate. The characterization of the pore shape and dimensions provides key information for estimating the flow and transport properties of fluids within the sintered agglomerate of those MSNs and for modeling the atomic MSN structures needed for pore-fluid simulations.