To study 48 h processing time of Polygoni Multiflori Radix on its contents and changes of chemical components. HPLC was used to determine the contents of various components in 22 Polygoni Multiflori Radix samples with different processing time, and then the fingerprint similarity analysis and clustering analysis were used for characteristics analysis. Results showed that the similarity was between 0.9-1.0, with good correlation between the samples. In the clustering analysis, the 22 Polygoni Multiflori Radix and processed Polygoni Multiflori Radix samples were classified into 4 types according to the composition changes. The results demonstrated that 4-5 h was the best processing time, providing references for quality control and further study of Polygoni Multiflori Radix.