Marine cobalt-rich (Co-rich) crusts are submarine critical metal resources with high economic value. In this study, detailed in-situ fine-scale morphological, mineralogical, and geochemical analyses were conducted on Co-rich crust from the Western Pacific. The Co-rich crust can be divided into three layers: (1) Layer 1 is the oldest anthracite layer and contacts with the substrate, showing a very dense laminated/columnar texture. Layer 1 can be further divided into two distinct sublayers: a lower black, massive, dense sublayer (Layer 1–1) and an upper black-to-brown sublayer (Layer 1–2). (2) Layer 2 is porous and locally vuggy, and its pore space is filled with a large amount of silicate detrital minerals and clay minerals. (3) Layer 3, on the top, is black and dense, with a dendritic, columnar/laminated texture. Co is very unevenly distributed throughout the whole crust, with three distinct Co-rich areas. Layer 3 is a typical hydrogenetic crust and has not undergone late alteration. The main processes for Co enrichment are specific adsorption-oxidation on Mn-oxides and the structural incorporation of Co3+ into Mn-oxide phases. The average Co content of the Layer 3 is much higher than that of the other two layers. The presence of abundant detrital and clay minerals, along with high levels of Al, Si, and Ti in Layer 2, indicates the incorporation of terrigenous material, resulting in a high average growth rate. However, these processes are not conducive to Co enrichment. In the phosphatized Layer 1, fluctuations in element content are significantly greater than in the upper, non-phosphatized layers. Phosphatization has resulted in the partial decomposition of the initial Co-rich micro-layers, which may have reactivated and migrated Co, contributing to secondary Co enrichment.