Rheum palmatum L. (R. palmatum L.) is a traditional Chinese herb and food, in which rhein and emodin are the main bioactive components. The extraction of the two compounds from R. palmatum L. is, thus, of great importance. In this work, protic ionic liquids (PILs) were applied in the microwave-assisted extraction (MAE) of rhein and emodin from R. palmatum L., which avoids the toxicity of organic solvents. The results of the present study indicate that PILs possessing higher polarity exhibit higher extraction ability due to their stronger absorption ability for microwave irradiation. Compared with conventional solvents, such as methanol, trichloromethane, and deep eutectic solvents (DESs), the PIL, 1-butyl-3-himidazolium methanesulfonate ([BHim]MeSO3) reported herein is more efficient. The selected extraction conditions of liquid–solid ratio, microwave irradiation time, microwave irradiation power, and PIL concentration were 40 g·g−1, 50 s, 280 W, and 80%, respectively. Under the selected conditions, the extraction yields of rhein and emodin were 7.8 and 4.0 mg·g−1, respectively. These results suggest that PILs are efficient extraction solvents for the separation of active components from natural products.