Background: Due to the deep tissue penetration and reduced scattering, NIR-II fluorescence imaging is advantageous over conventional visible and NIR-I fluorescence imaging for the detection of bone growth, metabolism, metastasis, and other bone-related diseases. Methods: Here, we designed bone-targeted heptamethine cyanine fluorophores by substituting the meso-carbon with a sulfur atom, resulting in a bathochromic shift and increased fluorescence intensity, which together enables NIR-II tail imaging. Results: The newly synthesized S-substituted heptamethine fluorophores demonstrated a high affinity for hydroxyapatite and calcium phosphate, which improved bone-specific targeting with signal-background ratios >3.5. Particularly, P800SO3-PEG showed minimum nonspecific uptake, and most unbound molecules were excreted into the urinary bladder. Histological analyses demonstrated that P800SO3-PEG remained stable in the bone for over two weeks and was incorporated into bone matrices. Interestingly, the flexible thiol ethylene glycol linker on P800SO3-PEG induced a promising photothermal effect, making this bone-targeted agent a potential theranostic imaging agent.Conclusions: P800SO3-PEG shows a high affinity for bone tissues, minimum nonspecific uptake in the major organs, and photothermal effect upon laser irradiation, making it promising as a targeted NIR theranostic agent for bone diseases.