The invention relates to a kit and method for extracting a microbial genome DNA by a magnetic bead method. The kit comprises a microbial preservation buffer solution, a bacteriolytic agent solution I, proteinase K, silica gel magnetic beads, isopropanol and an ethanol water solution, and further comprises a bacteriolytic agent II, a lysis adsorption solution and a reinforced scrubbing solution. The bacteriolytic agent II comprises MES, EDTA, Triton X-100, lysozyme and a lysozyme enhancer. The lysis adsorption solution comprises Tris-HCl, sodium chloride, EDTA, TrionX-100 and a nucleic acid separation and absorption promoter; and the reinforced scrubbing solution comprises Tris-HCl, lithium chloride and ethanol. By adopting the kit provided by the invention, cell walls of gram-positive bacteria and various fungi can be completely destroyed to form protoplasts, DNA of the protoplast cells can be rapidly released under the action of the lysis adsorption solution, the DNA is efficiently adsorbed on the silica gel magnetic beads, and after the DNA is washed by the scrubbing solution and eluted by an elution solution, microbial DNA with high concentration and purity can be obtained.