Carbon supported atomically dispersed transition metal–nitrogen (MNx) catalysts are promising for catalysis. Synthesis of such catalysts with high densities of MNx sites is an important task. In this work, a facile and scalable method by combining freeze drying and hard templating is presented for the synthesis of N-doped mesoporous carbon supported high-density and exclusive CoNx sites (denoted as CoNx-NMCs). The influences of the drying method (freeze drying and regular drying) on the aggregation of the silica pore forming agent, the precursor and metal species and the properties and performances of the resulted catalysts are investigated. The strong Co2+/histidine and silica/histidine interactions and the homogeneous distribution of the SiO2 nanoparticles for precursor physical isolation are essential to inhibit metal aggregation, sustain N dopant and generate high densities of CoNx sites. The CoNx-OMCs possess high surface areas (440–630 m2/g), uniform mesopores (~ 7 nm), high N contents (2.54–17.84 wt%) and abundant CoNx sites with high single cobalt atom loadings up to 1.7 wt%. The representative catalyst delivers outstanding catalytic performances for hydrogenation of a series of nitro compounds into amines with excellent conversions and selectivities and a high stability with H2 as the reducing agent and water as the solvent. A series of control experimental results clearly reveal the critical role of the CoNx sites for the chemoselective hydrogenation and clarify the influences of the properties of the catalysts on their performances. The work may provide a general approach and some insight for the development of atomically dispersed MNx catalysts with a high metal atom utilization efficiency for the purpose of various catalytic applications.