A pressurised liquid extraction (PLE) and high performance liquid chromatography (HPLC) method was developed for simultaneous quantification of six major flavonoids in edible flower of Hylocereus undatus. In order to achieve the baseline separation of two pairs of isomers, the HPLC conditions were optimised with different kind of reversed phase columns and mobile phase gradient programs. In addition, the solvent concentration, extraction temperature, extraction time and flush cycle for PLE were also optimised. Zorbax SB-C8 (100 × 2.1 mm, 1.8 μm) column was chosen with acetonitrile and water containing 0.1% trifluoroacetic acid as mobile phase, the six analytes were eluted with baseline separation. The calibration curves showed good linearity (r > 0.9994) with LODs and LOQs less than 0.90 and 3.60 ng respectively. The RSDs for intra- and inter-day repeatability was not more than 1.09% and 1.79% respectively. The overall recovery of the assay was 96.9-105.2%. The sample was stable for at least 12 h. The newly established method was successfully applied to quantify six flavonoids in different parts of "Bawanghua", and the commercial samples from different locations.