It is challenging to fabricate multimodal imaging nanoprobes with high penetration depth and long blood circulation. Herein, we present multifunctional fluorinated nanoprobes (CFPP NPs) containing in situ formed copper chalcogenide nanoparticles for 19F magnetic resonance imaging (MRI) and photoacoustic imaging (PAI). The formed hydrophilic copper chalcogenide nanoassemblies demonstrated easy excretion stemming from facile disassembly, enhanced photothermal ability, and novel localized surface plasmon resonance (LSPR) absorption (centered at 1064 nm) in the “biological transparent” region. Both 19F MRI and PAI render these CFPP NPs suitable for multimodal imaging with high penetration depth and low background. Moreover, the chemo-photothermal synergistic therapy results suggest great potential in multimodal nanoprobes for imaging-guided tumor therapy applications.