A series of novel Schiff base-linked imidazole naphthalimides were developed and their antimicrobial behavior demonstrated that compound 9i could effectively inhibit the growth of some tested strains, especially for MRSA (MIC = 0.003 μmol/mL), which was superior to the reference drugs. Bacterial membrane permeabilization, bacterial resistance and time−kill kinetic assays of compound 9i against MRSA manifested that it was able to permeate cell membrane, rapidly kill the tested strains and stall the development of bacterial resistance. Preliminary research revealed that compound 9i could form a steady complex with calf thymus DNA by intercalation mode. These results suggested that compound 9i could serve as a promising anti-MRSA candidate.