Selaginella sinensis (Desv.) Spring has been used for many years as traditional Chinese medicine (TCM) for many years. Recently, ionic liquids (ILs) have attracted great attentions in extraction and separation technology of TCM as a new green solvent. In this paper, microwave assisted extraction-IL (MAE-IL) that extracted amentoflavone (AME) and hinokiflavone (HIN) from Selaginella sinensis was reported for the first time. The contents of two biflavonoids were simultaneously determined by a high performance liquid chromatography (HPLC) method. After different ionic liquids were compared, it was found [C6mim]BF4 had a high selectivity and efficiency. Moreover, the important extraction conditions, including solid-liquid ratio, IL concentration, extraction time, microwave power and radiation temperature, were also investigated and optimized by response surface methodology (RSM) using AME and HIN yields as index. The results showed that the extraction yields of AME and HIN from S. sinensis were 1.96 mg/g and 0.79 mg/g, respectively, under the optimal process parameters (0.55 mmol/L, 300 W, 40 min, 1:11 g/mL and 48 °C). Compared with the conventional extraction methods, MAE-IL could not only achieve higher yield in shorter time, but also could reduce the consumption of solvent. This effective, rapid and green MAE-IL method was suitable for the extraction of AME and HIN.