Development of novel nanocatalysts for the highly efficient in situ synthesis of H2O2 from H2 and O2 in the electro‐Fenton (EF) process has potential for the remediation of water pollution. In this work, AuPd/carbon nanotube (CNT) nanocatalysts were successfully synthesized by the facile aggregation of AuPd bimetals on CNTs. Characterization by X‐ray diffraction, transmission electron microscopy, and X‐ray photoelectron spectroscopy indicated that pure AuPd bimetallic heterogeneous nanospheres (≈20 nm) were well dispersed outside the CNTs, which resulted in better catalytic performance than Pd/CNTs alone: 0.36 M H2O2 was synthesized; 0.05 M Fe2+ optimally initiated the EF process due to the superior in situ Fe2+ regeneration; and the organic pollutant removal reached 100 % at 37 min, with a pseudo‐first‐order kinetic constant k1=0.051 min−1. Moreover, structural insights before/after catalysis revealed that Au strengthened the construction of the nanocrystals, avoided negative deactivation caused by AuPd agglomeration, and immobilized the active Pd(111). The catalytic stability of AuPd/CNTs over ten cycles implied long durability and promising applications of this material.