Integrating multi-scale sites in a composite catalyst is vital to realize efficient electrocatalysis. Herein, a synergistic composite catalyst consisting of Co atomic sites and in-situ generated PtCo intermetallic compounds (IMCs) (o-PtCo@CoNC) is proposed through Co pre-anchoring and subsequent impregnation-reduction method. High loading of Co atoms provides a chance for in-situ generating PtCo ordered intermetallic compounds. The remaining Co single atoms and PtCo IMCs construct synergistic electrocatalytic micro-regions. Benefiting from the ordered structure, synergistic effect of PtCo IMCs and Co single atoms, o-PtCo@CoNC exhibits excellent electrocatalytic performance for oxygen reduction reaction (ORR) and hydrogen evolution reaction (HER) with mass activity of 1.21 A mgPt−1 (at 0.9 V) and 5.70 A mgPt−1 (at an overpotential of 100 mV), respectively. Besides, o-PtCo@CoNC delivers negligible loss of half-wave potential and overpotential during long-term stability test in acid solutions, with 13 mV decay after 50,000 potential cycles for ORR and a 2.7 mV decay after 20,000 potential cycles for HER. The integration strategy of single-atomic sites coupled IMCs paves the way for enhancing the activity and durability of Pt-based electrocatalysts.