Background Polygoni Multiflori Caulis, the dried caulis of Polygonum multiflorum Thunb., is one of the commonly used traditional Chinese medicines having antioxidant, anti-obesity, anti-inflammatory and antibacterial effects. Polygoni Multiflori Caulis used clinically or circulated on market have great differences in their diameters. However, to the best of our knowledge, no study has been reported on the qualities of Polygoni Multiflori Caulis with different diameters. Results Systematic HPLC/UV/MS chromatographic fingerprinting and quantitative analytical methods combined with principal component analysis were developed and applied to analyze different Polygoni Multiflori Caulis samples. The contents of 2,3,5,4′-tetrahydroxystilbene-2-O-β-D-glucoside, the chemical marker for quality control on Polygoni Multiflori Caulis specified in Chinese Pharmacopoeia (2010 edition), were found to have surprising relevance with the samples’ diameters for the first time. Conclusion The finding provides a scientific basis for collecting Polygoni Multiflori Caulis in the best time. Moreover, the diameter can be used as the criterion for quality control on Polygoni Multiflori Caulis as a preliminary step in the future. In addition, scores plot obtained from principal component analysis shows the obvious differences between unqualified Polygoni Multiflori Caulis samples and qualified ones visually, which can be used to single out the unqualified ones with qualified ones efficiently and immediately.