Co-rich ferromanganese nodules in the Western Pacific Ocean are rich in Mn, Fe, Co, Ni, Cu and other metal elements, which are newly discovered seabed solid mineral resources in recent years. They are heterogeneous geochemical and mineralogical aggregates. Co-rich ferromanganese nodules with a particle size of 6 cm record tens of millions of years of marine sedimentary history during their growth. Therefore, high-resolution analysis technology is urgently needed to reveal the paleo marine environmental information. In this study, we used a microscopic X-ray fluorescence spectrometer (μ-XRF) to scan the surface of C3BC1704 Co-rich ferromanganese nodule, and obtained in situ high-resolution multi-element signal intensity data, and evaluated the application quality of μ-XRF technology in Co-rich ferromanganese nodules for the first time. The results show that Mn, Fe, Ti, Co, Ca, Ni elements have sensitive signal intensity changes, and the data show relatively good normal distribution characteristics, which can be used for quantitative or semi quantitative analysis. The signals of Si, Cu, Al and other elements are weak, and their data show a left skewed normal distribution. It is suggested that the relevant data should be used for reference only. The amount of data obtained is huge and independent of each other. In this study, different elements are connected into the multi-dimensional matrix to realize the mathematical operation and screening between the location information and feature elements of the data. The distribution and variation characteristics of metal elements are understood, and the environmental changes in the growth process of cobalt rich nodules are revealed. The results show that Mn, Fe and other elements fluctuate violently in the growth layer, and the distribution of metal elements in the Co-rich ferromanganese nodules is extremely uneven, showing multiple genetic types of alternating micro layers and seven large growth cycles. The main body of the C3BC1704 Co-rich ferromanganese nodule is exposed to seawater, and its metal elements mainly come from seawater, which belongs to the typical hydrogenic types. Further quantitative analysis showed that the contents of Mn, Cu and Ni decreased synchronously from the inside to the outside, while the contents of Fe, Ti and co increased synchronously. It is indicated that the Co-rich ferromanganese nodules relatively tend to be enriched in diagenesis in the early stage and hydrogenises mainly in the late stage. The distribution and variation characteristics of metal elements clearly show the growth structure, reveal the environmental changes, and promote the construction of the metallogenic model of Co-rich ferromanganese nodules.