Despite extensive research on water oxidation catalysts over the past few decades, the relationship between high-valent metal-oxo intermediates and the O-O bond formation pathway has not been well clarified. Our previous study showed that the high spin density on O in Ru^V=O is pivotal for the interaction of two metal-oxyl radical (I2M) pathways. In this study, we found that introducing an axially coordinating ligand, which is favorable for bimolecular coupling, into the Ru-pda catalyst can rearrange its geometry. The shifts in geometric orientation altered its O-O bond formation pathway from water nucleophilic attack (WNA) to I2M, resulting in a 70-fold increase in water oxidation activity. This implies that the I2M pathway is concurrently influenced by the spin density on oxo and the geometry organization of the catalysts. The observed mechanistic switch and theoretical studies provide insights into controlling reaction pathways for homogeneous water oxidation catalysis.