Abstract: Cold-seep carbonates serve as reliable geological archives that preserve critical information on seepage activity and paleo-marine sedimentary environments. Their mineralogical and geochemical characteristics effectively record fluid sources and composition, seepage intensity, and redox conditions during past periods of active seepage. Although cold seeps are widely distributed in the Okinawa Trough of the East China Sea, the relationship between carbonate records and paleoenvironmental changes during past active periods in this region remains poorly understood. This study focuses on carbonate crusts from the active “Guanshan” seep site in the middle and northern Okinawa Trough, employing systematic mineralogical, elemental, and isotopic geochemical analyses to elucidate the environmental conditions during carbonate formation. The results demonstrate that the cold-seep carbonate crusts are predominantly composed of aragonite (average 58.3%). All samples exhibit moderately negative δ¹³C values (–40.4‰ to –28.4‰) coupled with highly enriched δ¹⁸O signatures (+4.0‰ to +5.8‰), indicating a thermogenic methane source and relatively high methane flux in the study area. The formation of Guanshan cold-seep carbonates was primarily driven by sulfate-driven anaerobic oxidation of methane (SD-AOM) near the seafloor, with gas hydrate dissociation likely enhancing seepage activity. These carbonates precipitated in a relatively oxic, shallow subsurface environment. Measurements of carbon and oxygen isotopes (δ¹³C, δ¹⁸O), coupled with rare earth element (REE) patterns, provide key constraints on the formation models of distinct cold seep carbonates.