A series of novel benzimidazole derivatives were synthesized and characterized by (1)H NMR, (13)C NMR, MS, IR and HRMS spectra. All the new compounds were screened for their antimicrobial activities in vitro by two-fold serial dilution technique. Bioactive assay manifested that the bis-benzimidazole derivative 11d and its hydrochloride 13b exhibited remarkable antimicrobial activities, which were comparable or even better than the reference drugs Norfloxacin, Chloromycin and Fluconazole. The interaction evaluation of compound 11d with bovine serum albumin (BSA) by Fluorescence and UV-vis absorption spectroscopic method showed that BSA could generate fluorescent quenching under approximately human physiological conditions by the prepared benzimidazole compound 11d as result of the formation of ground-state compound 11d-BSA complex. The thermodynamic parameters indicated that the hydrogen bonds and van der Waals forces played major roles in the strong association of benzimidazole 11d and BSA.