For the structure-activity relationship study on berberrubine derivatives, a series of compounds bearing 9-O-acyl- and 9-O-alkyl-substituents were synthesized and tested for antimicrobial activity against Gram-positive, Gram-negative bacteria and fungi. Octanoyl, decanoyl, lauroyl derivatives among the acyl analogs and hexyl, heptyl, octyl, nonyl, decyl, undecyl derivatives among the alkyl analogs showed strong antimicrobial activity against Gram-positive bacteria and fungi. As a whole, alkyl analogs were more active than acyl analogs for antimicrobial activity. Synthesized derivatives had no activity on Gram-negative bacteria. Too short or too long substituents decreased activity. These results suggest that the presence of lipophilic substituents with moderate sizes might be crucial for the optimal antimicrobial activity.