Negatively charged diamond nanoparticles are known to be generated in the gas phase of the hot filament chemical vapor deposition (HFCVD) process. However, the structures of these nanoparticles remain unknown. Also, the effect of charging on the stability of nanodiamond structures has not been studied experimentally. Here, by installing a capturing apparatus in an HFCVD reactor, we succeeded in capturing nanoparticles on the floating and grounded SiO, carbon, and graphene membranes of a copper transmission electron microscope grid during HFCVD. We examined the effect of charge on the crystal structure of nanodiamonds captured for 10 s under various conditions and identified four carbon allotropes, which are i-carbon, hexagonal diamond, n-diamond, and cubic diamond, by analyzing 150 d-spacings of ∼100 nanoparticles for each membrane. Nanoparticles captured on the floating membrane consisted mainly of cubic diamond and n-diamond, whereas those captured on the grounded membrane consisted mainly of i-carbon. Diamond particles deposited for 8 h on the floating silicon (Si) substrate exhibited an octahedron shape with well-developed facets, and a high-intensity 1332 cm⁻¹ Raman peak, whereas diamond particles deposited on the grounded Si substrate showed a spherical shape partially covered with crystalline facets with a broad G-band Raman peak. These results indicate that charging stabilizes the diamond structure.