The dynamic combined nanometer etching process of making nanometer pattern includes the following steps: A. processing the substrate to flat in atom level; B. modifying needle tip of atomic force microscope via dipping the needle tip in protein, DNA or other interested solution for several minutes and blowing to dry; C. controlling ambient temperature and humidity; and D. making nanometer patternvia scanning to image with the modified needle tip in the substrate surface to select required area, making nanometer image with the needle tip in the selected area, and re-scanning to image the madenanometer pattern with the needle tip to check the made pattern. The said technological process is superior, and may be used in making nanometer pattern on the surface of soft biological macro molecule and other matters.