Carboxyl-rich alicyclic molecules (CRAM) constitute a major fraction of marine refractory dissolved organic matter (RDOM). The role of specific microbial interactions in generating this recalcitrant pool remains underexplored. Here, we conducted a 90-day rigorously controlled laboratory experiments for characterizing dissolved organic carbon produced by coccolithophore Gephyrocapsa huxleyi, bacterium Ruegeria pomeroyi, and their co-culture. Compared to either monocultures, the co-culture produced substantially more diverse and complex CRAM, including 479 unique formulas enriched in higher molecular weight and lower heteroatom content. These co-culture derived molecules are widely distributed throughout the water column and contributed to 30.9% CRAM detected in marine environments. Our results provide molecular-level evidence that even a simplified bacteria-phytoplankton system can substantially amplify the production and persistence of RDOM. Despite the far greater complexity of natural microbial networks, this minimal interaction framework reveals a fundamental mechanistic link between microbial partnerships and long term ocean carbon storage.