Two kinds of boron and nitrogen co-doped carbon nanotubes (CNTs) dominated by bonded or separated B and N are intentionally prepared, which present distinct oxygen reduction reaction (ORR) performances. The experimental and theoretical results indicate that the bonded case cannot, while the separated one can, turn the inert CNTs into ORR electrocatalysts. This progress demonstrates the crucial role of the doping microstructure on ORR performance, which is of significance in exploring the advanced C-based metal-free electrocatalysts.