The oligotrophic northwestern Pacific Ocean (NPO) is characterized by pervasive nitrogen limitation that exerted principal control over primary productivity. Labile dissolved organic nitrogen (LDON) may serve as a crucial nitrogen source. Mesoscale eddies and seamount topography reshape habitat heterogeneity and regulate biogeochemical cycles via hydrodynamic disturbances, yet their effects on LDON metabolism are not clear. To fill this gap, we collected water samples from surface to 1500 m at eight stations covering centers of warm- and cold-eddies and the seamount region at the NPO during fall 2022, integrating geochemical, metagenomics and metatranscriptomics analyses to investigate LDON metabolic patterns and their regulatory mechanisms. Our results showed greater LDON turnover rates and metabolism-related gene abundances at seamount stations than those at eddy ones (p < 0.001). Such disparity stemmed from contrasting hydrodynamic regimes: seamounts maintained steady nutrient replenishment through topographic upwelling, introducing LDON into water. Greater substrate availability elevated LDON metabolic gene abundances and accelerated organic nitrogen remineralization and turnover. In contrast, eddies lacked sustained upward nutrient inputs to support equivalent LDON production, leading to lower substrate availability and slower LDON cycling. In surface waters of the warm-eddy stations, LDON metabolic gene abundances were relatively higher than those at cold-eddy ones. Anticyclonic warm eddies exhibit central downwelling limiting upward nutrient input, their oligotrophic surface conditions force microorganisms to utilize LDON as a nitrogen source. The elevated LDON gene abundances and expression below the DCM layer (p < 0.001) could result from enhanced substrate availability in deeper waters (e.g., zooplankton, protein degradation). Higher abundances of LDON metabolic genes and transcripts than those of nitrate transport genes (nrtABCD) indicated a community-level preference for LDON as nitrogen sources at the NPO. Alphaproteobacteria, Gammaproteobacteria and Cyanophyceae served as core microbial groups mediating LDON metabolisms. Overall, this study suggested that LDON was actively utilized and served as a major nitrogen source for microbial communities. LDON cycling was jointly structured by three hierarchical mechanisms: regional hydrodynamic disturbances that modulated the metabolic intensity, vertical environmental filtering that shaped depth-dependent functional patterns, and lineage-specific metabolic strategies that determined substrate utilization niches. These findings advanced the understanding of microbial responses to multi-scale dynamical disturbances in regulating nitrogen metabolisms.