The invention provides a dual process capable of removing heavy metal ions and carrying out microorganism deep anaerobic fermentation, which successfully solves the difficulty that the heavy metal content in the organic fertilizer exceeds standard, and simultaneously utilizes a heavy metal removing device to carry out microorganism deep anaerobic fermentation so as to shorten the production period of the organic fertilizer. The process not only is suitable for fertilizer production from domestic wastes, but also can be used for removing heavy metals in the production process of the organic fertilizer from raw materials containing organic wastes (organic matters), such as peat soil, sludge, subsidiary agricultural product wastes and the like. Particularly, by the adoption of the process, the treatment difficulty of the sludge with very high heavy metal content in various sewage treatment plants can be effectively solved, the raw material source of the organic fertilizer is increased, and the development of organic agriculture is promoted. The practical application in fertilizer production plant utilizing the domestic wastes proves that the process is feasible, and the effects of removing the heavy metal ions and carrying out microorganism anaerobic fermentation can reach the expectation.