Here we report a precise control of isolated single ruthenium site supported on nitrogen-doped porous carbon (Ru SAs/N-C) through a coordination-assisted strategy. This synthesis is based on the utilization of strong coordination between Ru3+ and the free amine groups (-NH2) at the skeleton of a metal organic framework, which plays a critical role to access the atomically isolated dispersion of Ru sites. Without the assistance of the amino groups, the Ru precursor is prone to aggregation during the pyrolysis process, resulting in the formation of Ru clusters. The atomic dispersion of Ru on N-doped carbon can be verified by the spherical aberration correction electron microscopy and X-ray absorption fine structure measurements. Most importantly, this single Ru sites with single-mind N coordination can serve as a semihomogeneous catalyst to catalyze effectively chemoselective hydrogenation of functionalized quinolones.