Abstract: Negative Chemical Ionization Mass Spectrometry (NCI-MS) is amenable to organic compounds with high electronegativity. However, nothing has previously been reported about the comparative study of a different reaction gas. In this paper, the methane, isobutane, ammonia, ammonia in methane, ammonia in isobutane as reaction gases for NCI are introduced. The effect factors of reaction gas pressure, source temperature, filament emission current and electron energy are evaluated for each high electronegativity pesticide considered in this study. Finally, the pure ammonia led to a remarkable reduction in background noise with a significant improvement for overall sensitivity of the method. Combining with ASE extraction, the limit of detection (LOD) for residue pesticides in soil is between 0.01-0.32 μg/kg, the recovery is 73.3%-108.1% and the RSD is between 2.5%~8.8%.