We developed a general and effective strategy to afford rod-like [Au25(SPh)5(PPh3)10X2]X2 (X = Cl/Br) nanoclusters, capped by conjugated delocalized pπ electron mediated ligands. The detailed atomic structure of these materials was resolved by synchrotron radiation X-ray diffraction (SRXRD) combined with electrospray ionization mass spectrometry (ESI-MS) and UV–vis analyses. The Au17(SR)3(PPh3)6X2 minimum asymmetric unit, with exposed Au atoms at the center, can serve as an important model to understand the transformation of homogold nanoclusters into alloy nanoclusters. The conjugated delocalized pπ electrons of the thiolate ligands can effectively tune the electronic properties of the Au25 kernel, as qualitatively evidenced by the energy gaps measured by UV–vis experiments and density functional theory (DFT) calculations. The delocalized electrons distinctly flow to the orbitals of the Au25 kernel via the S atoms of the aromatic thiolates. The ESI-MS analysis indicates that Au3 clusters are formed during the etching reactions, which provide an opportunity to gain insight into the intriguing conversion pathway of the Aun (PPh3)m Xy precursor to the final Au25 nanorods. Finally, the thiophenol-protected Au25 nanorods, immobilized on activated carbon, show good catalytic activity in the aerobic oxidation of glucose to gluconic acid (74% glucose conversion and 100% selectivity for gluconic acid), much higher than that of the aliphatic Au25 analogue. The Au25(SPh)5(PPh3)10X2 catalyst yields a turnover frequency (TOF) of 13.5 s–1, higher than that of commercial catalysts such as Pd/activated carbon (AC) and Pd-Bi/AC. The insight obtained from this study will support the development and design of efficient nanogold catalysts for special oxidation reactions.