Nanomaterials that engage in well-defined and tunable interactions with proteins are pivotal for the development of advanced applications. Achieving a precise molecular-level understanding of nano-bio interactions is essential for establishing these interactions. However, such an understanding remains challenging and elusive. Here, we identified stoichiometric interactions of water-soluble gold nanoparticles (Au NPs) with bovine serum albumin (BSA), unraveling their synergism in manipulating emission of nano-bio conjugates in the second near-infrared (NIR-II) regime. Using Au25(p-MBS)18 (p-MBS = para-mercaptobenzenesulfonic acid) as paradigm particles, we achieved precise binding of Au NPs to BSA with definitive molar ratios of 1:1 and 2:1, which is unambiguously evidenced by high-resolution mass spectrometry and transmission electron microscopy. Molecular dynamics simulations identified well-defined binding sites, mediated by electrostatic interactions and hydrogen bonds between the p-MBS moieties on the Au25(p-MBS)18 surface and BSA. Particularly, positively charged residues on BSA were found to be pivotal. By careful control of the molar ratio of Au25(p-MBS)18 to BSA, atomically precise [Au25(p-MBS)18]x-BSA conjugates (x = 1 or 2) could be formed. Through a comprehensive spectroscopy study, an electron transfer process and synergistic effect were manifested in the Au25(p-MBS)18-BSA conjugates, leading to drastically enhanced emission in the NIR-II window. This work offers insights into the precise engineering of nanomaterial-protein interactions and opens new avenues for the development of next-generation nano-bio conjugates for nanotheranostics.