This paper describes the application of atmospheric pressure gas chromatography quadrupole-time-of-flight mass spectrometry for the simultaneous determination of organophosphorus pesticides in apple, pear, tomato, cucumber and cabbage. Soft ionization with atmospheric pressure ionization source was compared with traditional electron impact ionization (EI). The sensitivity of GC coupled to atmospheric pressure ionization (APGC) for all the analytes was enhanced by 1.0–8.2 times. The ionization modes with atmospheric pressure ionization source was studied by comparing the charge-transfer and proton-transfer conditions. The optimized QuEChERs method was used to pretreat the samples. The calibration curves were found linear from 10 to 1000 μg/L, obtaining correlation coefficients higher than 0.9845. Satisfactory mean recovery values, in the range of 70.0–115.9%, and satisfactory precision, with all RSDr <19.7% and all RSDR values <19.5% at the three fortified concentration levels for all the fifteen OPPs. The results demonstrate the potential of APGC-QTOF-MS for routine quantitative analysis of organophosphorus pesticide in fruits and vegetables.