Atomic metal species based catalysts (AMCs) show remarkable potential in various catalytic reactions. The coordination configuration of the metal atoms has been widely recognized as the determining factor to the electronic structure and the catalytic activity. However, the synergistic effect between the adjacent layers of the multilayered AMCs is always neglected. We reported an atomic Co and Pt co-trapped carbon catalyst, which exhibits a ultrahigh activity for HER in the wide range of pH (η10=27 and 50 mV in acidic and alkaline media, respectively) with ultralow metal loadings (1.72 and 0.16 wt% for Co and Pt, respectively), much superior to the commercial Pt/C. Theoretical analysis reveals that the atomic metals on the inner graphitic layers significantly alter the electronic structure of the outmost layer, thus tailoring the HER activity. This finding arouses a re-thinking of the intrinsic activity origins of AMCs and suggests a new avenue in the structure design of AMCs.