The initial stages of formation of precursor clusters are considered in an evolving system containing various types of polyhedra: T tetrahedra and M polyhedra (pyramids, octahedra, and others). A graph topological representation of the precursor clusters of different self-organization levels of a chemical system is given. The model has been applied to find precursor clusters for Na,Ti-silicates that crystallize in the Na-Ti-Si-O(H) systems. For ramzaite Na₂Ti₂Si₂O₉ (RAM) and a dimorph of natisite (NAT), namely, paranatisite Na₂TiSiO₅ (PNAT), computer techniques (the TOPOS 4.0 program package) have been used to perform the full 3D reconstruction of structure self-assembly: precursor cluster-primary chain-microlayer-microframework (supraprecursor). New types of eight-polyhedral ring precursor clusters have been identified. The packing specifics of precursor clusters in crystal-forming microlayers determine the platy habit of Na,Ti-silicate single crystals.