Our earlier work showed that the stability of the bioactive compounds gastrodin (GA) and vanillyl alcohol (VA) in Gastrodia elata Blume behaved differently with varying compositions of water-ethanol using pressurized liquid extraction (PLE) at room temperature. To have a better understanding of the extraction process of these thermally labile compounds under elevated temperature conditions, pressurized hot water extraction (PHWE) and microwave-assisted extraction (MAE) methods were proposed. PHWE and MAE showed that GA and VA could be extracted using pure water under optimized conditions of temperature and extraction time. The extraction efficiency of GA and VA by the proposed methods was found to be higher or comparable to heating under reflux using water. The marker compounds present in the plant extracts were determined by RP-HPLC. The optimized conditions were found to be different for the two proposed methods on extraction of GA and VA. The method precision (RSD, n=6) was found to vary from 0.92% to 3.36% for the two proposed methods on different days. Hence, PHWE and MAE methods were shown to be feasible alternatives for the extraction of thermally labile marker compounds present in medicinal plants.