Nanodiamonds have outstanding mechanical properties, chemical inertness, and biocompatibility, which give them potential in various applications. Current methods for preparing nanodiamonds often lead to products with impurities and uneven morphologies. We report a two-step high-pressure high-temperature (HPHT) method to synthesize nanodiamonds using naphthalene as the precursor without metal catalysts. The grain size of the diamonds decreases with increasing carbonization time (at constant pressure and temperature of 11.5 GPa and 700 °C, respectively). This is discussed in terms of the different crystallinities of the carbon intermediates. The probability of secondary anvil cracking during the HPHT process is also reduced. These results indicate that the two-step method is efficient for synthesizing nanodiamonds, and that it is applicable to other organic precursors.