Understanding the chemical mechanism of crystal nucleation at the molecular level is crucial for the design of architectural structures of valuable materials in the future. In this study, it has been revealed that amorphous silicate precursors, which play a role in the nucleation processes of zeolitic frameworks, can be regularly fragmented in mass spectroscopy due to the hydroxyl functional groups in their molecular structures. In this way, by using the mass spectra acquired from LDI-TOF MS, the systematic evolution stages of a common 1D precursor converting to the 3D unit cells of MFI and MOR zeolite structures observed in the same reaction medium were constructed through a nucleation mechanism at the molecular level for the first time. Here we show a novel nucleation pathway that does not occur via stochastic assembly of atoms or distinct building blocks by molecular recognition. Each of the proposed nucleation mechanisms of these different frameworks carrying structural similarities is from different combinations of sequential self-attaching intramolecular covalent couplings of identical origin precursors. The dynamic molecular structure capable of forming finite building units of target frameworks during the nucleation process of this precursor, which is the polymerized form of simple 6-membered siloxane chains, has been arranged around structure directing agents before a hydrothermal reaction.