An accurate and sensitive method was established for the determination of polypeptide toxins amanitins and phallotoxins in the food containing wild edible mushrooms by liquid chromatography-triple quadrupole mass spectrometry. The toxins in sample matrix were extracted with hydrochloric acid solution (0.5% in water, v/v), cleaned by HLB cartridge and separated by C18 chromatographic column under basic condition (pH = 10.5). Amanitins and phallotoxins were monitored by an electrospray ionization source (ESI) under negative and positive modes, respectively, in one injection cycle. Basic mobile phase condition was applied to suppress the ionization efficiency of sodium ion adducts and improve that of the hydrogen ion adducts under ESI mode. The calculated limits of detection in sample matrix were 0.002–0.005 mg kg−1 and the limits of quantification were 0.005–0.01 mg kg−1. The linear range was 0.01–2 mg kg−1 with a correlation coefficient >0.996. The average recoveries at three spiking levels were 72.6%–91.8% with relative standard deviations of 5.2%–10.1% (n = 6). The developed method was applicable for the adulteration screening of inedible Amanitas in the food containing wild edible mushroom and the applicable adulteration markers were α-amanitin, β-amanitin and phallacidin.