In order to compare the phenolics in Salvia miltiorrhiza with different sources, the phenolics extracted from different sources were studied by chemical fingerprinting method, and salvianolic acid B as marker molecule was quantitatively analyzed. The results showed that the absolute amounts of phenolics in S. miltiorrhiza roots were seriously affected by different factors, such as origin, harvest time, root disease, root color, root diameter, and the part of plant. However, these factors had little influence on relative amounts of phenolics. The chemical fingerprinting of phenolics derived from different sources had high similarity. The content of salvianolic acid B harvested in August was the highest, and which was significantly reduced by diseases, such as root rot and nematode. Contents of phenolics in the brick red roots were the highest, compared to puce and white roots. The bigger the diameter, the higher contents of phenolics were. So, these could provide the basis for quality evaluation and resource utilization of S. miltiorrhiza.