Electrocatalytic two-electron oxygen reduction reaction (2e−-ORR) to produce hydrogen peroxide (H2O2) is a promising green way to replace the conventional anthraquinone reaction. Non-metallic catalysts are considered as low-cost catalysts due to their excellent stability and versatile surface chemistry. The performance of non-metallic electrocatalysts is usually limited by the limited catalytic active sites on the surface. Here, we report fluorine and boron dual-doped carbon nanotubes (B–F–C) as a metal-free electrocatalyst for H2O2 production, fabricated via a fast microwave treatment. With the synergistic effect of F and B, this strategy can effectively convert carbon and boron atoms on carbon nanotubes into highly active sites. As a result, an H2O2 yield up to 24.3 mol g−1 L−1 is achieved over B–F–C with a stable selectivity of above 90% within 0.2–0.7 V vs. RHE in 0.1 M KOH. Density functional theory (DFT)calculations further confirm that the multiple active sites created by the dual doping of fluorine and boron are the key factor in improving the performance of 2e−-ORR electrocatalysis. Therefore, this work offers a promising prospect for the design and preparation of catalysts with high catalytic activity for H2O2 production and other catalytic areas of industrial significance.