In this work, a fast and efficient microwave-assisted extraction (MAE) method was developed to extract main bioactive alkaloids from lotus plumue. To optimize MAE conditions, three main factors were selected using univariate approach experiments, and then central composite design (CCD). The optimal extraction conditions were as follows: methanol concentration of 65%, microwave power of 200 W, and extraction time of 260 s. An high performance liquid chromatography-diode array detector (HPLC-DAD) method was established to quantitatively analyze these phytochemicals in different lotus plumule samples and in different part of lotus. Chromatographic separation was carried out on an Agilent Zorbax Extend-C column (4.6 mm×150 mm, 3.5 µm). Gradient elution was applied with the mobile phase constituted with 0.1% triethylamine in water (A) and acetonitrile (B): 40%−70% B at 0−8 min, 70%−100% B at 8–9 min, 100% B for 2 min, and then equilibrated with 40% B for 2 min.