This paper presents a quantitative analysis of the relations of the occurrence of polymetallic nodules with the geochemical actions of microbes in the seawater, pore water and sediments at the bottom of the eastern Pacific Ocean basin. Emphasis is laid on the relations of the activity intensity and biochemical transformation rate of aerobic bacteria (iron bacteria, Thiobacillus thioparus, halobacteria and manganese-oxidizing bacteria) and anaerobic bacteria (sulphate-reducing bacteria, denitrifying bacteria, Thiobacillus denitrificans) with mineralization. The experimental research on the migration and accumulation of ore-forming elements caused by microbial and chemical actions shows that the microbes have changed the conditions of oxidation and reduction in the system, and their effect on the element precipitation is much stronger than the chemical actions and accelerates the enrichment of Fe and Mn. It demonstrates that the microbes can change the environment to promote the accumulation of ore-forming elements, thus leading to indirect mineralization.It is first found under the scanning electron microscope (SEM) and transmission electron microscope (TEM) that there are fossil microbes of various sizes and forms in the shells of polymetallic nodules, and even ultramicrofossil bacteria at the cores. On the walls of some mineralized microbes there are sheaths of Fe and Mn oxides. After the death of the microbes, their bodies are accumulated on the interface of seawater-sediments and form polymetallic nodules. Microstructures of polymetallic nodules formed by microbes are also discussed, and two modes of microbial minerogenesis of polymetallic nodules, both direct and indirect, are suggested in the paper.