Organic molecules that emit near-infrared (NIR) fluorescence at wavelengths above 1000 nm, also known as the second NIR (NIR-II) biological window, are expected to be applied to optical in vivo imaging of deep tissues. The study of molecular states of NIR-II dye and its optical properties are important to yield well-controlled fluorescent probes; however, no such study has been conducted yet. Among the two major absorption peaks of the NIR-II dye, IR-1061, the ratio of the shorter wavelength (900 nm) to the longer one (1060 nm) increased with an increase in the dye concentration in tetrahydrofuran, suggesting that the 900 nm peak is due to the dimer formation of IR-1061. Both absorption peaks are also observed when IR-1061 is encapsulated in the hydrophobic (stearyl) core of micellar nanoparticles (MNPs) of a phospholipid-poly(ethylene glycol). The dimers in the MNP cores decreased via dimer dissociation by enhancing the mobility of the hydrophobic stearyl chains by heat treatment of the dye-encapsulating MNPs at 50-70 °C. The MNPs maintained the dissociated IR-1061 monomers in the core after recooling to 25 °C and showed a higher NIR-II fluorescence intensity than those before heat treatment. This concept will provide better protocols for the preparation of NIR-II fluorescent probes with well-controlled fluorescence properties.