Crystallization of zeolite ZSM-39 (MTN), a clathrate and silicate analogue of the 17 Å cubic gas hydrate, was examined in a solvent system involving a tetramethylammonium chloride – 1,6-hexanediol deep eutectic mixture and significant amount of water. The crystallization process was followed by powder X-ray diffraction (PXRD), and solid-state nuclear magnetic resonance (SSNMR) techniques involving several nuclei such as 19F, 29Si, and 13C. The results indicate that the crystallization starts from the arrangement of amorphous Si–O–Si species around the tetramethylammonium ions and subsequent formation of the cages in the precursors similar to [51264] cages in the MTN topology. The larger [51264] cages are then connected via the smaller [512] cages containing the fluoride ions to form the final MTN structure. Scanning electron microscopy (SEM) and atomic force microscopy (AFM) analyses show that the crystal growth rates along <100> and <111> directions are roughly the same, suggesting that the (100) and (111) planes have similar stability under the crystallization conditions used. AFM study also shows that the freshly born nuclei on the (100) face are of a height of 2 nm, suggesting a layer by layer growth of the polyhedral crystal.