Aurones and indanones were proved to be potential antibacterial agents in our recent work. Based on strategy of bioisosterism and diene insertion, a series of aurone and indanone derivatives were designed and synthesized, then submitted to the antibacterial activity evaluation on C. albicans, E. coli and S. aureus. According to the results, nineteen of thirty synthesized compounds had inhibitory activity against at least one bacterium. The minimum value of MIC activity was 62.5 µM (A2, B1, B3, B4, B8, C6, D1, D2) and the minimum value of MBC was 62.5 µM (B4, C6). In addition, molecular docking and ADMET prediction were also applied to the possible binding mode and the druggability of active compounds. Our research once again demonstrated that aurone and indanone are good scaffolds for the development of antibacterial agents, especially against S. aureus bacterial.