Abstract: From studies on the methane seep carbonates, three different layer structures among them are found. Micro-structure, chemical components and minerals have been researched. The results show that the carbonate nodules have different microstructures, but the chemical components have no great changes. The carbonate chimneys have two layer types.one is parallel to the chimney wall, which has different min-erals and lithification, and the other is perpendicular to the chimney wall, which has different carbonate mineral contents. The different layers reflect the changes of geology, geophysics, geochemistry and biology when the carbonate formed, so it is helpful to reconstruct the paleoenvironment.