The standards of plant toxins were separated by a C18 column with gradient elution with 0.1% formic acid/water (V/V) and 0.1% formic acid/acetonitrile (V/V) as mobile phase and acquired by ion mobility-quadrupole time of flight mass spectrometry (IM-QTOF MS) in positive ion mode. A database of 308 plant toxins including retention time, collision cross-section (CCS) and its fragment ions was established. Honey dissolved in water or herbal beverage was extracted by acetonitrile and purified with PSA sorbent, and then acquired by ultrahigh-performance liquid chromatography IM-QTOFMS. The acquired data were processed by comparing with the database we established to confirm the target compounds. The average recoveries for samples at two levels ranged from 60.6% - 120.1%, with relative standard deviation (n = 6) less than 25%. The limit of quantitation for plant toxins ranged from 1 - 20 μg/kg. The developed screening method was used in determination of honey, herbal beverage and honey flavored tea beverage samples. The results showed that berberine was detected in one honey with 1 μg/kg and caffeine was present in some beverages with the concentration from 200 and 5500 μg/kg. This method could meet the requirement for rapid screening of plant toxins in honey and herbal beverage. It can be used for the quality control of honey and herbal beverage in enterprises or quality inspection departments. It also can be used in the rapid screening of food poisoning.