The invention discloses a kit for extracting fecal microbial genome by magnetic bead method and an extraction method thereof, belongs to the field of biotechnology; the technical scheme adopted is; akit for extracting fecal microbial genome by magnetic bead method include lysis fluid, impurity removal reagent, genomic adsorbent and eluent, in buff a, B and C combine lysis microorganisms, the humic acid and other impurities are removed by the unique precipitating solution, then adsorbing genomic DNA with magnetic beads, further removing foreign proteins and salt ions with special buffer G andbuffer H, and finally eluting the purified genomic DNA; a method for extract genomic DNA of faeces microorganism includes such step as extracting genomic DNA of faeces microorganism with high efficiency and sufficient quantity, extracting genomic DNA of faeces microorganism with high quality, extracting genomic DNA of faeces microorganism with simple procedure, high speed, safety and no pollution,shortening extracting time, and can be used for manual operation and automatic platform, and is widely suitable for extracting animal faeces genomic DNA of faeces microorganism with high speed, efficiency and economy for customers, and has wide application prospect.