We report the multifunctional nanocomposites (NCs) consisting of F-19-moieties grafted Cu7S4-Au nanoparticles (NPs) for negligible background F-19 magnetic resonance imaging (F-19-MRI) and computed tomography (CT) imaging guided photothermal therapy. The localized surface plasmon resonance (LSPR) absorption can be reasonably tuned to the in vivo transparent window (800-900 nm) by coupling Au (<10 nm, LSPR 530 nm) with Cu2S4 (<15 nm, LSPR 1500 nm) into Cu2S4 Au heterodimers. The in vivo photothermal tests show that Cu2S4 Au show deeper light penetration with 808 nm irradiation, better photothermal efficacy, and less damage to normal tissues than Cu2S4 with 1500 nm irradiation, Moreover, compared to traditional 'H-MRI, the F-19-MRI based on these NCs demonstrates much better sensitivity due to the negligible background. This work offers a promising strategy for multimodal imaging guided photothermal therapy of deep tissue with good efficacy.