Abstract: A method of microwave assisted extraction was set up and optimized based on Ionic Liquid (IL-MAE) for the determination of amentoflavone in Selaginella doederleinii.The effect of factors on the yield of amentoflavone was investigated through the single factor and orthogonal test, including ionic liquid concentration, microwave power, solid-to-liquid ratio, extraction time and extraction temperature.The best extractive method was obtained to compare with ethanol microwave-assisted extraction and alcohol refluxing extraction on the yield of amentoflavone.The results showed that, the best conditions were as follows:2.0 mmol/LC₆ mim PF₆for extraction solvent, solid-liquid ratio of 1:15 (g/mL), microwave power of 500 W, temperature of 50℃, microwave extraction time of 40 min.The yield of amentoflavone was 0.61% ±0.08% and the extraction method significantly increase amount of target (p < 0.05), which compared with the other two methods. This proved that IL-MAE would be a fast, efficient and green method to extract amentoflavone from Selaginella doederleinii.