The marine nitrogen cycle plays a crucial role in regulating primary productivity, particularly in oligotrophic waters, where endogenous recycled nitrogen often serves as the primary driver of phytoplankton growth. Microzooplankton (20–200 μm), as the core of the microfood web, are considered an important source of recycled nitrogen through their metabolic activities; however, systematic quantitative studies on the spatiotemporal dynamics between their release rates and phytoplankton growth remain limited. In the spring of 2025, this study conducted in-situ cultivation experiments at nine stations in typical oligotrophic waters of the western Pacific (the Philippine Sea Basin and the Mariana Trench). Using ¹⁵N stable isotope dilution techniques, the study simultaneously measured microzooplankton community structure, the regeneration rates of ammonium nitrogen and urea nitrogen, and the biomass responses of phytoplankton across different size classes. The results indicate that the ammonium regeneration rate (mean 0.357 ± 0.012 μmol N L⁻¹ h⁻¹) was significantly higher than the urea regeneration rate (mean 0.600 ± 0.519 nmol L⁻¹ h⁻¹) (p < 0.05), with ammonium exhibiting greater spatial stability. Twenty-four hours after nitrogen source addition, potential primary productivity increased significantly, with the increase in the urea-added group (0.669 mg C m⁻³ h⁻¹) exceeding that in the ammonium-added group (0.464 mg C m⁻³ h⁻¹), and the phytoplankton community structure shifted toward smaller particle sizes (pico-sized). Correlation analysis indicated that nitrogen regeneration rates were closely associated with microzooplankton biomass and physicochemical parameters of the water column, suggesting that the metabolic activity of microzooplankton plays a key role in meeting the nitrogen demands of oligotrophic ecosystems. This study provides a preliminary systematic quantification of the rates of ammonium and urea recycling mediated by microzooplankton in oligotrophic waters of the western Pacific Ocean, as well as their differential effects on phytoplankton growth, thereby offering critical field data to support the development of improved parameterization schemes for nitrogen recycling processes in marine nitrogen cycle ecodynamic models.