The fingerprints of Rhizoma coptidis from various sources were established by ultra performance liquid chromatography (UPLC) and the anti-bacterial activities of R. coptidis on Escherichia coli (E. coli) growth was studied by microcalarimetry. The UPLC fingerprints were evaluated using similarity analysis (SA) and hierarchical clustering analysis (HCA). Some quantitative parameters obtained from the thermo-genic curves of E. coli growth affected by R. coptidis were analyzed using principal component analysis (PCA). The spectrum-effect relationships between UPLC fingerprints and anti-bacterial activities were investigated using canonical correlation analysis (CCA). The results showed that close correlation existed between the spectrum-effect relationships. Berberine, jateorrhizine and palmatine in the UPLC fingerprints might be the main anti-bacterial components. The anti-bacterial activities of R. coptidis were related with the main active constituents, along with the production place and the harvesting time of this herb, the latitude and longitude of the place. This work provides a general model of the combination of UPLC and microcalorimetry to study the spectrum-effect relationships of R. coptidis, which can be used to discover principle components of it on bioactivity.