Helium is almost the only choosable carrier gas used in gas chromatography-mass spectrometry (GC-MS). A mixed standard solution of five organophosphorus pesticides was analyzed by using GC-MS, and hydrogen or helium as carrier gas, so as to study the feasibility of hydrogen instead of helium as carrier gas for the determination of organophosphorus pesticides. Combining a mass spectrum database built by ourselves, the results were deconvolved and identified by Automated Mass Spectral Deconvolution & Identification System (AMDIS32), a software belonging to the workstation of the instrument. Then, the statistical software, IBM SPSS Statistics 19.0 was used for the clustering analysis of the data. The results indicated that when hydrogen was used as carrier gas, the peaks of the pesticides detected were slightly earlier than those when helium used as carrier gas, but the resolutions of the chromatographic peaks were lower, and the fraction good indices (Frac. Good) were lower, too. When hydrogen was used as carrier gas, the signals of the pesticides were unstable, the measuring accuracies of the pesticides were reduced too, and even more, some compounds were undetectable. Therefore, considering the measuring accuracy, the signal stability, and the safety, etc., hydrogen should be cautiously used as carrier gas in the determination of organophosphorus pesticides by GC-MS.