The inhibitory effect of three berberine alkaloids (BAs) from Coptis chinensis Franch, a traditional Chinese medicinal (TCM) herb, on Bifidobacterium adolescentis growth was investigated by microcalorimetry. The power-time curves of B. adolescentis with and without BAs were acquired, meanwhile the extent and duration of inhibitory effect on the metabolism were evaluated by the growth rate constant (k), half inhibitory ratio (IC50), maximum heat-output power (P (max)), peak time of maximum heat-output power (t (p)) and total heat production (Q (t)). k, P (max) and Q (t) decreased, and t (p) was prolonged with the increase of BAs concentration. The IC50 of BAs is 806 mu g/mL for berberine, 341 mu g/mL for coptisine and 236 mu g/mL for palmatine. The sequence of antimicrobial activity of BAs is berberine < coptisine < palmatine. Combined with previous studies, it could be shown that the sequences of antimicrobial activity of BAs on both Bacillus shigae and Escherichia coli are berberine > coptisine > palmatine. The structure-function relationship of BAs indicates that the functional group methylenedioxy or methoxyl at C2 and C3 might be the major group inducing the activities of BAs on E. coli and B. adolescentis. Meanwhile, the substituent groups at C2, C3, C9 and C10 almost have equal effect on B. shigae.