Single-atom catalysts (SACs) with their unique electronic and geometric structures usually exhibit extraordinary catalytic performance for many important chemical reactions. Herein, a modular strategy is used to decorate isolated cobalt sites into a multichannel carbon matrix (Co@MCM) with Co content of about 1.4 wt% for efficient electrochemical reduction of oxygen. As confirmed by X-ray absorption fine structure investigation, the pre-designed CoN4 configuration and geometric structure are well maintained in the newly developed Co@MCM. The decorated CoN4 units together with the multichannel carbon substrate with high conductivity and porosity endow the catalyst with excellent activity for the oxygen reduction reaction (ORR). Our findings not only present some fundamental insights for the accurate modulation of nanostructured catalysts at the atomic scale, but also reveal the structural origin of the enhanced catalytic activity.