As compared with the ordinary landfill cover material, clay soil, the effect of methane stress on oxidation rate and microbial community structure was investigated in waste soil (material from biologically treated municipal solid waste). The results showed that the moisture content of the clay soil was low, due to the low water retaining capacity. As environmental temperature and rainfall changed, the clay soil caked and inhibited methanotrophs growth. However, with a high organic matter, water-holding capacity and porosity, the waste soil provided a favor condition for methanotrophs growth and propagation. After exposure to methane flow for 120 days, methane oxidation potential in the middle and bottom layers of the waste soil column increased to 11.25-13.48 micromol/(g x h), which was 10.4-24.5 times higher than that in clay soil column. The topsoils were both found to be dried and inhibit methane oxidation. Methane oxidation (removal) efficiency by the waste soil column reached 48.3% at the end of the experiment, which was 5-6 times higher than that by the clay soil column. The amounts of the phospholipid fatty acid (PLFA) biomarks 16:1 omega 8c and 18:1 omega 8c for Type I and II methanotrophs, respectively, showed that a strong linear relationship was observed between methane oxidation potential and PLFA 18:1 omega 8c content in soil samples.