N-Alkylated benzimidazole derivatives have been synthesized via the aza-Michael addition reactions of 1H-benzimidazoles to α,β-unsaturated compounds in water and palladium acetate obviously promoted these transformations. The reported method, overcoming the inactivation of palladium under the equivalent nitrogenous conditions, has the advantages of convenient manipulation, atom-economy, as well as environmental friendliness. The bioactive results showed that butyl 3-(5,6-dimethyl-1H-benzo[d]imidazol-1-yl)propanoate (3c) exhibited excellent inhibitory activity against Bacillus subtilis (MIC=16μg/mL) and Bacillus proteus (MIC=8μg/mL). Therefore, this process would facilitate the construction of various potential bioactive compounds based on the benzimidazole scaffold under mild conditions.