Object To study the microwave assisted procedure for the extraction of baicalin from root of Scutellariae baicalensis Georgi Methods An MSP 100D domestically made microwave sample preparation system with a maximum power of 850 watts was used. The effects of solvents, pressure/temperature of solvents and microwave radiation time on the yield of baicalin were studied by orthogonal experimental design. Results The optimal experimental conditions were extraction at 70% of microwave power with 30 times of 35% ethanol at a constant heating pressure/temperature of 0.15 MPa for 30 s. Conclusion The microwave assisted extraction not only takes a shorter time with better parallel results, but also gave an increased yield of about 10% as compared with ultrasonic extraction.