The high expense associated with electrocatalysts poses a challenge to the advancement of a hydrogen-based energy economy. The utilization of nonprecious metal-based electrocatalysts that are easily prepared and cost-effective is imperative for the future sustainability of a hydrogen society. The semiconductive MoO3-x has been identified as a promising nonprecious electrocatalyst for the hydrogen evolution reaction (HER). Nevertheless, enhancing its relatively low electrocatalytic activity toward HER remains a top priority. This study illustrates the manipulation of surface ammonium ions (NH4+) to produce uniform and distinct cobalt nanoparticles (Co NPs) on active MoO3-x supports, resulting in a more effective heterostructured composite electrocatalyst for HER. The presence of NH4+ ions in the MoO3-x film was extensively examined using infrared spectroscopy, X-ray photoelectron spectroscopy, and UV-visible colorimetric techniques. Additionally, the firmly attached NH4+ ions were employed as binding sites to precipitate Co-containing complex ions. Due to the monolayer-like adsorption of NH4+ ions, only a small quantity of Co precipitate was formed, which was subsequently electrochemically transformed into Co atoms that diffused and created well-separated uniform metallic Co nanoparticles (with an average size of less than 10 nm) on the MoO3-x film. The resulting heterostructure displays a 4.5-fold increase in current density for HER compared to the MoO3-x electrocatalyst through electrochemical assessments. The enhanced catalytic activity was ascribed to the optimized adsorption/desorption of the species involved in water reduction at the heterointerfaces and improved charge transfer rates. These nanoheterostructures hold great promise for a variety of applications in heterogeneous electrocatalysis, while the novel approach could potentially direct the creation of more heterostructures.