Ultrasmall atomically precise thiolate-protected gold nanoclusters with surface open sites are crucial for practical applications in catalysis. However, there is a lack of systematic studies that unify the kernels-isomerization, modification of peripheral ligands and electronic effects into one system, as well as their correlation to catalytic performances. In this work, three structurally related Au 25 nanoclusters with reported star Au 25 kernels, Au 25 -i-FTP, Au 25 -bi-FTP, and Au 25 -bi-CHT have been synthesized through two different methods: one-pot direct reduction and two-step reduction by using AsPh 3 as converter. Their structures and catalytic performance have been comparatively investigated. Au 25 -i-FTP has a classic Au 13 core capped by six dimeric RS-Au-SR-Au-SRs, while Au 25 -bi-FTP and Au 25 -bi-CHT feature typical rod-shaped biicosahedral geometric kernel. All of the three Au 25 clusters were effective catalysts for oxidation of organosilanes, different from conclusions obtained in literature. Especially, the nanorod-type Au 25 -bi-CHT clusters protected by flexible thiol ligands showed very good catalytic performance in this reaction, the conversion and selectivity were close to 100% within 5 min. The ligand rigidity and electron effects work together to modulate the catalytic properties. The findings inspire us to rethink kernel and ligand effects on catalytic property, and the principle demonstrated here will possibly be widely-used in high active atom-precise catalysts modification.