<p>Traditional carbonate factories (<i>e.g.</i>, Schlager’s tropical factory, cool-water factory, and mud-mound factory) primarily focus on carbonate depositional environments. In contrast, cold-seep carbonate factories highlight microbial-mediated authigenic carbonate formation within siliciclastic-dominated sedimentary settings, offering a novel paradigm for understanding marine carbon cycling. This review article systematically synthesizes the key geochemical fingerprints of cold-seep carbonates, including carbon-oxygen isotopic compositions, trace element enrichment patterns, and metal stable isotope characteristics, to establish diagnostic criteria for identifying cold-seep carbonates. These signatures not only aid in distinguishing cold-seep carbonates but also serve as critical tools for tracing paleo-seep activity and evaluating its impacts on marine carbon cycling. Research indicates that precipitation processes in cold-seep carbonate factories typically exhibit strongly negative δ¹³C anomalies, relatively enriched δ¹⁸O values, and anomalous enrichment of trace elements (<i>e.g.</i>, Mo, U, REEs). Additionally, metal stable isotopes (<i>e.g.</i>, Mo, Sr, Ca) can constrain the redox conditions and fluid sources in cold-seep environments. The formation of cold-seep carbonate factories is closely linked to modern carbon cycling, acting not only as a short-term carbon sink for methane sequestration but also potentially influencing deep-time carbonate sedimentary dynamics. Future studies should integrate high-resolution analytical techniques, geochemical numerical simulations, and interdisciplinary approaches to decode the evolution of cold-seep systems and explore their potential roles in achieving carbon neutrality.</p>