We successfully developed an antimicrobial assembly (Mo154/TK-14) using molybdenum-polyoxometalate and a positively charged peptide of TK-14. It was characterized and assayed using zeta-potential, dynamic light scattering (DLS), and TEM measurements. The Mo154/TK-14 assembly showed an enhanced 808 nm absorption and, therefore, improved the photothermal conversion efficiency of Mo154 (30.3%) to 38.6%. Consequently, in comparison to 5 μM Mo154 without irradiation, both the biofilm formation and bacterial viability of S. aureus were 24.6% and 20.2%, respectively, for the Mo154/TK-14 assembly; the biofilm formation and bacterial viability were further decreased to 7.7% and 4.4% under 808 nm irradiation, respectively. Therefore, the Mo154/TK-14 assembly reflects convincing antibacterial properties compared to Mo154. This is due to the synergistic effect between the peptide-binding enhanced 808 nm absorption and the improved PTT properties. The antimicrobial assembly offers a novel strategy for the rational design of light-responsive antibacterial materials.