The worldwide increase in bacterial antibiotic resistance has led to a search for alternative antibacterial therapies. The present study reports the development of yolk-structured multifunctional up-conversion nanoparticles (UCNPs) that combine photodynamic and sonodynamic therapy for effective killing of antibiotic-resistant bacteria. The multifunctional nanoparticles (NPs) were achieved by enclosing hematoporphyrin monomethyl ether (HMME) into its yolk-structured up-conversion core and covalently linked rose bengal (RB) on its silica (SiO) shell. Excitation of UCNPs with near-infrared (NIR) light that has improved penetration depth for photodynamic therapy (PDT) enabled the activation of HMME and RB and thus the generation of singlet oxygen (O). The SiO layer, which improved the biocompatibility of the UCNPs, surrounded the yolk structure, with a cavity space which had a high efficiency of loading photosensitizers. Synergistic PDT and sonodynamic therapy (SDT) improved the photosensitizer utilization rate. As a result, a greater inhibition rate was observed when antibiotic-resistant bacteria were treated with a combined therapy (100%) compared with either the PDT (74.2%) or SDT (70%) alone. Our data indicate that the multifunctional NPs developed in this study have the potential for use in the clinical synergistic PDT-SDT treatment of infectious diseases caused by antibiotic-resistant bacteria.