Based on the regulations of the Ministry of Health and Welfare (MOHW) of Taiwan in 2017, an analysis of 373 pesticides in food was conducted using the MOHW official method. The analyses involved the use of either liquid chromatography mass spectrometry (LC-MS) with electrospray ionization (ESI) or gas chromatography mass spectrometry (GC-MS) with electron ionization (EI). In this study, the applicability of detecting pesticides using atmospheric pressure chemical ionization (APCI) was investigated and evaluated. The pesticides were separated using an aqueous solution of ammonium formate with methanol as the mobile phase, and ionization efficiency was compared between APCI, ESI, and EI coupled with triple quadrupole mass spectrometer using multiple reaction monitoring (MRM) acquisition. Among the 196 pesticides that were originally analyzed by ESI, 164 could be successfully detected by APCI with 6 showing a higher sensitivity when APCI was used. Among the 177 pesticides that were analyzed by EI, 43 could be successfully detected by APCI. The results also showed that APCI gave superior ionization efficiency for pesticides containing triazine, imidazole, triazole, and pyrazole groups.