A strain Aspergillus spp. F1 which could effectively metabolized omethoate was screened out in this study. F1 tended to form granula with diameter 4–5 mm after 5 days culture in shaker. The pH range from 4.5 to 6.5 was the suitable pH range for growth and metabolism of Aspergillus spp. F1. The maximum omethoate removal rate was about 3.0 mg/(h L), and the removal fraction of omethoate reached 90% after 8 days culture when initial concentrations of omethoate were not more than 2000 mg/L in medium. There was no obvious relativity between cell growth and cometabolism of omethoate. Starch was the best carbon source for omethoate removal and the result after 3 days reached 56.6% removal. F1 could use omethoate to metabolize as single nitrogen or phosphate source. The residual fragments in medium after treatment with the Aspergillus spp. F1 were determined by gas chromatography–mass spectrometry. The analysis results showed that only fragment o,o,s,-trimethyl phosphorothioate (TEP) containing phosphorus was available and the fragment containing nitrogen was consumed by F1 thoroughly in culture process. But no accumulations of TEP were observed in the omethoate bioremediation process. F1 could effectively remove omethoate in complex nutritional environment safely.