The land−sea interface is a vital component of global biogeochemical cycles, where microorganisms drive the cycling of carbon, nitrogen, and sulfur. This review synthesizes the research progress from representative land−sea interfaces to elucidate how the microbial community structure and metabolic function influence the mobilization, transformation, and retention of organic carbon. Here, we also review the mechanisms underlying carbon cycle dynamics and emphasize the role of coupled biogeochemical cycles and climate change. A key focus is the synergistic interaction among the marine microbial carbon pump (MCP), the soil MCP, and the mineral-associated carbon pump, hereafter referred to as the land−sea MCP framework. We further propose an integrated study framework, based on measurable parameters such as carbon use efficiency and bacterial growth efficiency, to link microbial processes to long-term carbon sequestration at the land−sea interface.