Dissolved organic carbon (DOC) is one of the largest active carbon pools in the ocean, yet the extent to which its molecular composition regulates microbial metabolism remains poorly understood. We investigated the relationships between dissolved hydrolyzable amino acid (DHAA) composition, heterotrophic bacterial production (BP), and extracellular enzymatic activities (EEA) in the southwest Indian Ocean. DOC and DHAA concentrations decreased with depth as the organic matter shifted from Leu-rich, protein-like forms to Gly-enriched degraded forms. The BP:DOC ratio, used here as a proxy for carbon utilization efficiency (CUE), increased with Leu mol% but decreased with Gly enrichment. Partial correlation analyses showed that the relationship between Leu mol% and BP:DOC remained significant after accounting for DOC concentration and depth. With increasing organic matter degradation, microbial communities shifted from growth-oriented metabolism toward enzyme-mediated resource acquisition, reflected by increasing cell-specific extracellular enzyme activities (EEA) relative to BP in deeper waters. Nitrogen-acquiring enzymes consistently exceeded carbon-acquiring enzymes across stations and depths, implying strong microbial demand for nitrogen relative to carbon in the ocean interior. Our results demonstrate that amino acid composition is not only an indicator of organic matter degradation but also an active regulator of microbial metabolic strategy, linking substrate biochemistry to microbial carbon processing and long-term carbon storage in the ocean.