Phase transformation between carbon allotropes usually requires high pressures and high temperatures. Thus, the development of low‐temperature phase transition approaches between carbon allotropes is highly desired. Herein, novel amorphous carbon nanocapsules are successfully synthesized by pulsed plasma glow discharge. These nanocapsules are comprised of highly strained carbon clusters encapsulated in a fullerene‐like carbon matrix, with the formers serving as nucleation sites. These nucleation sites favored the formation of a diamond unit cell driven by the self‐nanoscopic local excessive pressure, thereby significantly decreasing the temperature required for its transformation into a diamond nanocrystal. Under moderate electron beam irradiation (10–20 A cm⁻²) without external heating, self‐organization of the energetic carbon clusters into diamond nanocrystals is achieved, whereas the surrounding fullerene‐like carbon matrix remains nearly unchanged. Molecular dynamics simulations demonstrate that the defective rings as the active sites dominate the phase transition of amorphous carbon to diamond nanocrystal. The findings may open a promising route to realize phase transformation between carbon allotropes at a lower temperature.