Rational design and controlled fabrication of novel electrochemical interfaces are intriguing approaches to improve the intrinsic electrocatalytic performance of nanocatalysts towards energy applications. Herein, we demonstrated an in situ thermal phosphorization strategy based on MoO₃-adenine (MoAD) hybrids for the construction of crystallographically interconnected nitrogen-doped molybdenum phosphide (N–MoP) nanocrystals consisting of abundant grain boundaries for high-efficient hydrogen evolution reaction (HER). In this strategy, MoAD hybrids were synthesized through a hydrothermal reaction, for which adenine was used as both the nanostructure inducer and the nitrogen source. The as-synthesized tandem N–MoP nanocrystals exhibited remarkable HER activity, with overpotentials of 125 and 175 mV at a cathodic current density of 10 mA cm⁻² and corresponding Tafel slopes of 69 mV dec⁻¹ in alkaline and acidic conditions. It was found that the HER catalytic performance could be significantly influenced by the crystallinity of MoP nanostructures. The work presented here will not only unravel the potential of adenine in nanocatalysts development but also reinforce the exploitation of the sustainable raw materials for disparate nanocatalysts.