Manganese nodules, which are mainly composed of manganese and iron oxide, show the structure of annual rings. Chemical compositions vary widely, such as the concentrations of Co, Ni and Cu, and the relative ratio of Mn/Fe. It may be possible to analyze the old environmental changes from the chemical composition. In this study, characterization of the chemical composition of manganese nodules was performed to find the factors concerning the effect of a changing of environment. In the sample, a characteristic layer was found in a raster image of X-rays by SEM-EDX. In this layer, the abundances of iron and sulfur were high, but manganese was low. In this particular structure, pyrite should be considered to occur as very small particles. Further, manganese nodules were examined along the structure of annual rings in more detail for chemical composition, which confirmed the result of SEM-EDX. The main elements were analyzed by an inductively coupled plasma atomic emission spectrometer (ICP-AES), and trace elements were analyzed by an inductively coupled plasma mass spectrometer (ICP-MS). As a result, the distribution of the elements changed to 1/3 from 1/2 and 3/4 from the center. The distribution of the elements changed one after another at the former. The latter agreed with the section at which there was sulfur when analyzed by SEM-EDX. The distribution of the elements suddenly changed at the same time at the latter. Therefore, we can guess that the different changes of the environment occurred twice.