Mussels are widely distributed in global waters, from offshore shallow waters to hydrothermal vents and cold seeps in the deep oceans. Mussels secrete calcium carbonate and form shells to protect their soft tissues. The nancomposite properties of mussel shell and the application prospects in biomaterial, tissue engineering and bionics have attracted much attention of scientists. The Raman spectroscopy is a kind of non-destructive, non-contact, simultaneous multi-component analysis detection technique, and can provide mineral information of samples. The mineral composition and distribution patterns of the shells and the nacre layers of the mussels collected from four different study sites (cold seeps in the Southwest of Taiwan, Desmos hydrothermal Field, Laboratory rearing, and Dalian-offshore) were obtained using the confocal Raman technique. The results showed that both of the prismatic layer and the nacre layers of the mussels are calcium carbonate. The Raman shifts of the primatic layers locate at 711 and 281 cm-1 indicating the mineral composition of prismatic layer is calcite. The mineral composition of nacre exists difference in different environment although the shell nacre is mainly calcium carbonate: the mineral of nacre in Dalian-offshore is aragonite. The Raman shifts of aragonite are at 706 and 206 cm-1. Aragonite crystallizes poor. The mineral of nacre layers grown in hydrothermal field and cultured in laboratory are aragonite (706 and 206 cm-1) with good crystallization. The mineral of mussel nacre in cold seep is aragonite (706 and 206 cm-1) and contains a little calcite. The Raman shifts of calcite are at 711 and 281 cm-1. Taking the living environment conditions into consideration, the results suggested that difference in the mineral composition and distribution patterns in the mussel shells are probably caused by different physical and chemical properties within the four environments. Moreover the nacre layers is more sensitive to the pressure change of living environment. Our work also showed that the Raman spectroscopy is a quick and effective technique that can be used to analyze the mineral composition of mussels in different environments and may shine some lights on the study of the life processes and adaptive mechanisms of mussels in deep oceans.