Density functional theory calculations have been performed to investigate how different nucleophiles and directing groups affect the preference of C−H versus C−O bond functionalization in the ruthenium-catalyzed coupling reactions of aryl ethers with organoboronates. Our results indicate that the preference depends on the relative stability of the transition state structures for the C−O bond activation in the C−O bond functionalization pathway and the transmetalation with boronate to form a Ru−C bond in the C−H bond functionalization pathway. When the transition state structure for the transmetalation with boronate lies lower in energy than that for the C−O bond activation, C−H bond functionalization is preferred, and vice versa. How different nucleophiles and directing groups affect the relative stability of the transition structures has been discussed in detail.