Gynostemma pentaphyllum (Thunb.) Makino, also known as jiaogulan, has been shown to have antioxidant, antiproliferative, and anti-inflammatory activities. Flavonoid is considered a major contributor for these beneficial effects. To obtain chemical patterns of flavonoids in G. pentaphyllum of different genotypes (di- versus tetraploids) and different parts (leaf versus whole plant) of plants, the extraction condition was optimized and a fingerprinting approach was established by means of high-performance liquid chromatography coupled with diode array detection and mass spectrometry (HPLC-DAD-MS). Eight flavonoids were identified, among which rutin and quercetin were quantified. The highest levels of rutin and quercetin were 23.03 and 12.10 mg/g, respectively, observed in the diploid leaf sample 2L3 and 2L2, while the lowest levels of rutin and quercetin were 1.92 and 0.25 mg/g in the tetraploid whole-plant sample 4W3. The chemical patterns were further analyzed by similarity calculation and principal component analysis (PCA). Seven common characteristic peaks were found in all of the tested samples. Flavonoid patterns of tetraploids were significantly different from those of diploids, whereas different parts of plants showed less difference. The flavonoid pattern of the diploid leaf sample was most similar to that of the reference botanical G. pentaphyllum. The combination of chromatographic fingerprint and quantification analysis could be used for quality assessment of G. pentaphyllum and its derived nutraceutical products.