Abstract: Boiling processing is commonly used in post-harvest handling of White Paeony Root (WPR), in order to whiten the herbal materials and preserve the bright color, since such WPR is empirically considered to possess a higher quality. The present study was designed to investigate whether and how the boiling processing affects overall quality of WPR. First, an ultra-high performance liquid chromatography quadrupole/time-of-flight mass spectrometry-based metabolomics approach coupled with multivariate statistical analysis was developed to compare the holistic quality of boiled and un-boiled WPR samples. Second, ten major components in WPR samples boiled for different durations were quantitatively determined using high performance liquid chromatography to further explore the effects of boiling time on the holistic quality of WPR, meanwhile the appearance of the processed herbal materials was observed. The results suggested that the boiling processing conspicuously affected the holistic quality of WPR by simultaneously and inconsistently altering the chemical compositions and that short-time boiling processing between 2 and 10 min could both make the WPR bright-colored and improve the contents of major bioactive components, which were not achieved either without boiling or with prolonged boiling. In conclusion, short-term boiling (2-10 min) is recommended for post-harvest handling of WPR.