The novel quaternary ammonium modified magnetic carboxyl-carbon nanotubes (QA-Mag-CCNTs) have been synthesised and characterized. QA-Mag-CCNTs were applied in magnetic dispersive solid phase extraction (Mag-dSPE) for preconcentration of perchlorate from tea leaves prior to liquid chromatography-tandem quadrupole mass spectrometry (LC-MS/MS) analysis. The Mag-dSPE procedure for preconcentration of perchlorate succeed in overcoming the flaw (containing target analyte randomly) of commercially available SPE cartridge. Under optimal conditions, the results showed higher extraction efficiency of QA-Mag-CCNTs, with recoveries between 85.2% and 107%. And the satisfactory precision with inter-day and intra-day RSD values were lower than 8.0%. Furthermore, QA-Mag-CCNTs were evaluated for reuse up to 20 times. The limit of quantification (LOQ) for perchlorate was 8.21 ng kg−1. The developed method was successfully applied in tea leaves for food-safety risk monitoring in Zhejiang province, China. The results showed the concentrations of perchlorate in 229 out of 240 collected samples were in the range of 0.082–988 μg kg−1. It was confirmed that QA-Mag-CCNTs were highly effective materials used for preconcentration of perchlorate. Display omitted •QA-Mag-CCNTs have been synthesised and characterized by SEM, VSM and XPS.•QA-Mag-CCNTs are evaluated in Mag-dSPE for preconcentration of perchlorate from tea leaves.•It succeeds in overcoming the flaw (containing perchlorate randomly) of SPE cartridge.•The Mag-dSPE procedure is environmental friendly and effective to remove matrix.•Mag-dSPE LC-MS/MS method is efficient and promising for food-safety risk monitoring.