Objective To optimize the extraction process of free anthraquinones from Rheum Emodi Wall. with microwave technique. Methods Single factor and orthogonal test design were used to investigante the effects of the four main factors including microwave power, alcohol concentration, extraction time and the ratio of materials and solution on the extraction efficiency of free anthraquinones. Results Using 70% ethanol solution in high-fire and the ratio of materials and solution of 1∶8 for 5 min to extract two times, the extraction rate of Rhubarb anthraquinones was 1.31% and the relative rate was 88.52%. Conclusion Microwave extraction method is high efficient, easy and timesaving for extracting anthraquinones in Rheum Emodi Wall..