Abstract: Coral reefs thrive in oligotrophic waters, and their health is highly dependent on the "holobiont" composed of the coral host, Symbiodiniaceae, and symbiotic microorganisms. Current coral research primarily focuses on the interactions between the coral host and microorganisms, while the mechanisms underlying bacteria–Symbiodiniaceae interactions remain poorly understood. Nitrogen is a key element for maintaining healthy coral growth, yet its concentration is extremely low in oligotrophic environments, suggesting that the symbiotic system possesses unique adaptation strategies to nitrogen limitation. To investigate the specific mechanisms of bacteria–algae interactions within this strategy, this study established an algae–bacteria co-culture system and combined it with metabolomics to analyze metabolic changes in the microbial community. The results revealed that under nitrogen-limited conditions, the bacterial community in the co-culture system significantly upregulated multiple amino acid biosynthesis pathways and enhanced the synthesis and secretion of plant hormone-like substances such as indole-3-acetic acid (IAA). This study elucidates the potential mechanisms of microbial synergy in response to nitrogen limitation from a metabolic interaction perspective and provides a theoretical basis for the conservation and restoration of coral reef ecosystems.