Fluorescence imaging in the second near-infrared (NIR-II) window, which offers the advantages of deep tissue penetration and high spatial resolution, is emerging as a promising modality for monitoring biomolecules in living systems. However, a major challenge remains in the development of NIR-II fluorophores with improved luminescence efficiency. In this study, the underlying mechanisms of naphthalene-substitution strategy for enhancing the fluorescence quantum efficiency (FQE) of NIR-II fluorophore are systematically investigated using a computational approach that integrates density functional theory with thermal vibration correlation function method. Based on a molecular framework featuring benzobisthiadiazole (BBTD) as the acceptor, two novel naphthyl-substituted derivatives are constructed by replacing the phenyl group adjacent to the BBTD moiety at the α- and β-positions. Photophysical characteristics reveal that incorporation of the naphthalene moiety results in both an enlarged energy gap and a hypsochromic emission in the fluorophore. Notably, the largely suppressed nonradiative relaxation induced by the increased adiabatic excitation energy and reduced vibration coupling is mainly responsible for the luminescence efficiency enhancement in the naphthyl-contained compounds. As a result, C1-βNaphth achieves a 4.2-fold FQE enhancement on the premise of efficient NIR-II emission, enabling it to be a potential high-performance NIR-II chromophore. These findings establish a rational design strategy for optimizing the luminescent properties of NIR-II dyes, thereby facilitating the development of highly efficient fluorophores for bioimaging applications.