Organophosphorus pesticides (OPs) in apple and tomato were determined by using fast gas chromatography-mass spectrometry (FGC-MS) coupled with auto-headspace solid-phase microextraction (SPME). The experimental conditions of FGC were investigated and developed. Three different fibers were studied and compared and it was found that the polydimethysiloxane (PDMS) was the best. Factors affecting the extract efficiency, such as extraction time, temperature, ion strength, agitator speed, and content of organic solvents, were investigated and optimized. The limits of detection (LOD) of OPs were achieved between 0.002 ng/g and 0.955 ng/g; the RSD was less than 20.9%, and the recoveries were from 79% to 117%. For most commercial fruit samples, ultra trace residues of OPs were found, mainly on the surface, and their concentrations were generally lower than LOD of conventional methods.