Here, a novel β-cyclodextrin (β-CD) based trace matrix solid-phase dispersion (MSPD) method was developed to extract isomers from different honeysuckle samples using ultrahigh performance liquid chromatography. The structures of the analytes were characterized and determined via quadrupole time-of-flight tandem mass spectrometry and nuclear magnetic resonance. Under optimum conditions, 25mg of sample was dispersed with 75mg of β-CD, and 0.5mL of methanol was used as the elution solvent. The proposed method produced a good linearity (r(2)>0.99) for the isomers, with limits of detection ranging from 1.62 to 3.33ng/mL. The average recovery values that were obtained from analyzing the spiked samples were calculated to be in the range of 87.04-105.20%. Moreover, the trace MSPD method required less reagents and a shorter extraction time in comparison with the traditional pharmacopoeia method and other reported approaches. The developed method was successfully applied for the determination of three real honeysuckle samples that were collected from different cultivated areas.