Bi2MoO6 (BMO) nanoparticles (NPs) have been widely used as a photocatalyst to decompose organic pollutants, but their potential for photodynamic therapy (PDT) is yet to be explored. Normally, the UV absorption property of BMO NPs is not suitable for clinical application because the penetration depth of the UV light is too small. To overcome this limitation, we rationally designed a novel nanocomposite based on Bi2MoO6/MoS2/AuNRs (BMO-MSA), which simultaneously possesses both the high photodynamic ability and POD-like activity under NIR-II light irradiation. Additionally, it has excellent photothermal stability with good photothermal conversion efficiency. The as-prepared BMO-MSA nanocomposite could induce the germline apoptosis of Caenorhabditis elegans (C. elegans) via the cep-1/p53 pathway after being illuminated by light with a wavelength of 1064 nm. The in vivo investigations confirmed the ability of the BMO-MSA nanocomposite for the induction of DNA damage in the worms, and the mechanism was approved by determining the egl-1 fold induction in the mutants that have a loss of function in the genes involved in DNA damage response mutants. Thus, this work has not only provided a novel PDT agent, which may be used for PDT in the NIR-II region, but also introduced a new approach to therapy, taking advantage of both PDT and CDT effects.