The heat-mediated reflux apparatus extraction of Paeonia lactiflora Pall. has been widely used as a traditional extraction method. In this paper, the microwave apparatus extraction method of Paeonia Radix was performed and the active ingredients and functional constituents were compared with the reference extraction method. The most effective extraction condition of albiflorin using the microwave was 120°C in 50% methanol, and paeoniflorin was maximally extracted at 60°C. The reduced level of paeoniflorin molecule at high-pressure and high-temperature extraction condition was caused by the molecular instability. Additionally, the microwave extraction of 50% methanol extracts at 150°C showed the highest functional constituents determined by in vitro DPPH radical scavenging activity, polyphenol concentration, and tyrosinase inhibition assay. The microwave apparatus was adapted as a rapid, low-cost, and environmentally friendly method to extract active ingredients and the practical extraction conditions of Paeonia Radix can be used in industrial applications.