The ability to control the charge and spin states of nitrogen-vacancy (NV) centers near the diamond surface is of pivotal importance for quantum applications. Hydrogen-terminated diamond is promising for long spin coherence times and ease of controlling the charge states due to the low density of surface defects. However, it has so far been challenging to create negatively charged single NV centers with controllable spin states beneath a hydrogen-terminated surface because atmospheric adsorbates that act as acceptors induce surface holes. In this study, we optically detected the magnetic resonance of shallow single NV centers in hydrogen-terminated diamond through precise control of the nitrogen implantation fluence. Furthermore, we found that the probability of detecting the resonance was enhanced by reducing the surface acceptor density through passivation of the hydrogen-terminated surface with hexagonal boron nitride without air exposure. This control method opens up new opportunities for using NV centers in quantum applications.