<p>Clarifying the oyster’s carbon budget of their farming ecosystem defines this industry’s future. Through biodeposition, oyster enhances the vertical flux of organic carbon. However, the cycling of sedimented carbon before being separated from the biosphere remains unclear. Here, we constructed the chronologic profiles of the sediment cores from a typical oyster farm with approximately 50 years of farming history. The profiles corresponded with the farming development, environment, associated biogenic elements, and microbial communities. Our results showed the organic carbon burial flux after the onset of intensive farming increased 2.6-fold, reaching 106 g C·m⁻²·yr⁻¹. Farming development drove the accumulation of microbial necromass, while the percentage of recalcitrant organic carbon in sediment organic carbon also increased from 42.52% to 60.19%. This study highlights the enhancement of carbon storage in response to the development of oyster farming, contributing to the understanding of the ecosystem-based carbon budget for oyster farming.</p>