Abstract: Phospholipid fatty acid (PLFA) as microbial molecular target was used to investigate the impact of different inputs of methamidophos (C2H8ONPS) on soil microbial community. Compared to the control soil, there was an increase of 0.85 nmol/g in the bacterial PLFAs and a decrease of 0.87 nmol/g in the fungi PLFAs, respectively. Our results represented that microbial biomass was not affected significantly by methamidophos. A significant reduction in fungal abundance and a selection of resistant bacterial population constituted the dynamic equilibrium of soil microbial community structure. The changes of soil microbial community structure might be due to H+ provided by methamidophos.