A micelle-mediated extraction technique, i.e. ionic liquid-based microwave-assisted extraction (ILs-MAE) technique has been developed for the effective extraction of podophyllotoxin from three Chinese medicinal plants. Several operating parameters were successively optimized by single-factor and L(9) (3(4)) orthogonal array experiments. 1-Butyl-3-methylimidazolium tetrafluoroborate ([bmim][BF(4)]), 1-decyl-3-methylimidazolium tetrafluoroborate ([demim][BF(4)]) and 1-allyl-3-methylimidazolium tetrafluoroborate ([amim][BF(4)]) were selected as the optimal surfactants for Dysosma versipellis, Sinopodophyllum hexandrum and Diphylleia sinensis, respectively. Compared with other extraction techniques, such as ionic liquids-based maceration extraction (ILs-ME), heat extraction (ILs-HE) and ultrasound-assisted extraction (ILs-UAE), the ILs-MAE technique not only took a shorter time but also afforded a higher extraction rate of podophyllotoxin from the herbs. Reversed phase high performance liquid chromatography was employed for the analysis of podophyllotoxin. The results showed that the linearity for analyzing podophyllotoxin in all three herbs was in the concentration range of 0.005-0.4 mg mL(-1) with the correlation coefficient between 0.9993 and 0.9996. LODs were 2.05-2.58 μg mL(-1) and RSDs of inter-day stability were less than 5.8%. Repeatability and intermediate precision were separately lower than 3.3% and 6.3%. The recoveries for podophyllotoxin extracted with the ILs-MAE technique were in the range of 97.1-102% and all RSDs were lower than 3.0%. Furthermore, the mechanism of ILs-MAE was preliminarily studied by means of kinetic mechanism, surface structures and chemical compositions of samples before and after different extraction techniques. On the basis of the destruction of herb surface microstructures and high solubility of ILs, the ILs-MAE technique eventually got the maximum yield value.