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The precisely coupling of metal nanoparticles with support domain are crucial to enhance the catalytic activity and stability of supported metal nanoparticle catalysts (MNPs). Here we selectively anchor Pd nanoparticles to the sp2 domain in graphene-based aerogel constructed with base-washed graphene oxide (BGO) by removing oxidative debris (OD). The effects of OD on the size and chemical composition of Pd nanoparticles in aerogels are initially unveiled. The removal of OD nanoparticles prompt selective coupling of Pd nanoparticles to the