•39 phytotoxins and mycotoxins in blood and urine were extracted with methanol and analyzed by HPLC-Orbitrap MS.•The sample processing is easy to operate, and a single analysis can be completed within 30 min.•It provides a basis and reference for the related research of public health poisoning analysis. Poisonings caused by plant toxins and mycotoxins occur frequently, which do great harm to human health and social public health safety. When a poisoning incident occurs, biological samples are commonly be used to conduct the detection of toxic substances and their metabolites for targeted clinical treatment and incident analysis. To establish an efficient and accurate analysis method of 39 phytotoxins and mycotoxins in blood and urine by high performance liquid chromatography quadrupole tandem orbitrap mass spectrometry (HPLC-Orbitrap MS). After 3 mL of methanol being added to 1 mL blood and urine respectively for extraction and protein precipitation, the supernatant was injected into HPLC-Orbitrap MS for analysis. The phytotoxins and mycotoxins were separated by Hypersil GOLD PFP column with gradient elution using methanol-5 mmol/L ammonium acetate as mobile phase. The data were collected in ESI positive ion mode using Full MS/dd-MS2 for mass spectrometry detection. The mass database of 39 phytotoxins and mycotoxins was developed, and accurate qualitative analysis can be obtained by matching with the database using the proposed identification criteria. Limit of detections (LODs) were 1.34 × 10−4 ∼ 1.92 ng/mL and 1.92 × 10−4 ∼ 9.80 ng/mL for blood and urine samples, respectively. Limits of quantification (LOQ) of toxins in blood and urine ranged from 4.47 × 10−4 ∼ 6.32 ng/mL and 6.39 × 10−4 ∼ 32.67 ng/mL, respectively. Intra-day relative standard deviations (RSDs) were 0.79 % ∼ 10.90 %, and inter-day RSDs were 1.08 % ∼ 18.93 %. The recoveries can reach 90 % ∼ 110 % with matrix matching calibration curves. The established method is simple and rapid to operate, which can complete the sample analysis within 30 min, providing technical support for clinical poisoning treatment and public health poisoning analysis.