Abstract: In order to understand the mechanism of lethal effect of magnetic-field on microbes, it is necessary to probe the changes of microbes treated by magnetic fields at the micro-level. Selecting Escherichia coli, Staphylococcus aureus and Saccharomyces cerevisiae as test targets, this article evaluated the alteration of four biological characteristics of microbes after being treated with the self-made generator of two-pole alternating magnetic fields. These four characteristics included the morphology of microbes under environmental scanning electron microscopy, the structure of microbes under transmission electron microscope, the relative absorbance at 260 nm of cell leakage materials, electrophoresis of DNA. The results show that the two-pole alternating magnetic fields can induce the damage of cell wall and membrane of the three microbes, the leak of cell contents, and the changes of DNA structure.