A rapid HPLC-UV method for the determination of three organic acids (neochlorogenic acid, chlorogenic acid, and cryptochlorogenic acid) in Polygoni Vivipari Rhizoma (PVR) by one marker was developed. The sample was prepared by effervescence-assisted matrix solid-phase dispersion (EA-MSPD). The separation of compounds was performed on a Poroshell column. The equal absorption wavelength was set as follows: 292 nm (0∼7 min) and 324 nm (7∼10 min). The analytical time including sample extraction and HPLC separation time was 12 min. The analytical method validation such as accuracy (recoveries 99.85%–106.29% and RSD < 2.9%), precision (RSD < 1.3%), reproducibility (RSD < 1.7%), and stability tests (RSD < 0.7% in 24 h) proved that the established HPLC method was suitable for determination of three organic acids in PVR. The contents of three analytes obtained by the external standard method with three markers and the equal absorption wavelength method with one marker were similar (RSD ≤ 2.0%). The developed method, which is rapid and reference compound saving, is an improved quality evaluation method of PVR.