The isolation of bioactive compounds from natural sources using conventional solvents has always suffered from the poor extraction ability and tedious extraction procedure. Ionic liquids (ILs) have emerged as the alternatives to conventional solvents due to their high extraction ability and low-toxic nature. In this work, a series of protic ILs was prepared via acid-base reaction using non-to-mild toxic organic acids and bases as starting materials. The synthesized protic ILs in combination with microwave-assisted extraction (ILs-MAE) were used to extract rosmarinic acid (RA) from Perilla seeds. Optimal extraction conditions were 5% of IL concentration, 50 s of microwave irritation time, 350 W of microwave irritation power and 50 g g−1 of liquid–solid ratio. Acidity of ILs and the extraction temperature played an important role in the extraction process. Compared with heating reflux extraction (HRE), ultrasound-assisted extraction (UAE) and maceration (MAC), the IL-MAE exhibited highest extraction ability and fastest extraction rate. After extraction, the IL could be recycled without losing its extraction ability via back extraction of RA with ethyl acetate. The RA in the ethyl acetate extract was further purified by column chromatography and high purity of RA (90.4%) could be obtained. These findings suggest that IL-MAE is promising method for the isolation of bioactive compounds from natural plants.