The study purpose was to develop experimental and theoretical models of the structure of cement stone modified with additives of various compositions. These models took into account the solid phase and pore space of cement stone, while the structure components had four levels of dispersity, such as nano-, micro-, submicro- and macro-. Polycarboxylate superplasticizer and three types of mineral additives such as silica fume, expanding sulfoaluminate modifier, and microcalcite, were the modifiers of cement systems. It was found that the silica fume and expanding sulfoaluminate modifier provided the possibility of changing the content of hydrate phases of cement stone, in particular, calcium silicate hydrates (C–S–H), portlandite, and ettringite. In particular, the use of expanding sulfoaluminate modifier led to an increase in the ettringite content in the cement stone volume by 2.0–3.3 times. At the same time, modification of the material with silica fume allowed to reduce the Ca(OH)2 volume concentration in the cement stone by 71–79% relative to the control compositions.