Well-ordered mesoporous silica nanoparticles with uniform hexagonal disk shapes are synthesized under dilute alkaline conditions with a two-step process, separating the nucleation and growth process. The resulting monodisperse hexagons can be arranged in a 2-dimensional (2D) ordered periodical super-structure. The hexagonal symmetry is similar in both scales. A statistical mechanical cell model is applied to analyze consequences of the interesting packing structure, including osmotic bulk modulus, phase separation and defects.