The micro-organisms of plant roots, wetland filler and wetland soil of subsurface flow wetland consumptive municipal sewage treatment plant effluents bypass test systems, in Changzhou City, north of the city sewage treatment plant, were studied through microscopic examination, urease, phospholipid fatty acid (PLFA) and other analytical tools for related seudies to reveal the characteristics and mechanism of micro-organisms with Subsurface Flow Wetland consumptive municipal sewage treatment plant effluents. The results showed that plant roots, filler contained rotifers, amoeba and other protozoa and Volvox, Volvox used the N, P and other pollutant of tail waters through photosynthesis biological metabolism, removal of N、P, etc, under conditions of low-carbon. The average content of wetland urease(N) was about 22.43 mg/g, the activity of urease was linearly related to the removal of TN, the higher the activity, the higher the removal rate of TN. Saturated fatty acid (PLFA) content was 99.30%, unsaturated fatty acid content was only 0.70% in Wetland fillers, which with subsurface flow wetland treatment PLFA contents of municipal sewage is very different (76.97% and 23.03%, respectively). The amount of fatty acid biomarker as an indicator, reveal wetlands matrix formed with aerobic bacteria was dominant structure of microbial ecology. Volvox, aerobic microorganisms was the main carriers of microbial removal of TN and other pollutants in low carbon source tail water.