We present a direct observation of the transformation of dense amorphous carbon clusters into diamond nanocrystalline under electron beam irradiation by in situ transmission electron microscopy, where the surrounding carbon matrix did not significantly change. Our findings provide clear and convincing evidence for the diamond nanocrystalline evolving from energetic amorphous carbon sites. Furthermore, graphitization of amorphous carbons usually demands a high temperature combined with high pressure. Hence, graphitization of amorphous carbons at relatively low temperatures is highly desired. Here we offer a useful method for catalyst-free graphitization of amorphous carbons by employing moderate electron beam irradiation, without external heating being applied.