For heterogeneous catalysts with nitrogen doped carbon materials as supporting substrates, accurate nitrogen (N) species and content is an important factor for promoting the catalytic activity. In this paper, N-doped graphdiyne (NGDY) was prepared from tetraethynylpyrazine (TEP) by bottom-up synthesis method as the support of metal nanoparticles. Specific pyridine nitrogen atoms are introduced in the N-doped carbon material. This unique structure makes it a promising material to support ultrafine metal particles or clusters. Microwave-assisted anchoring of Pd, Pt, Cu, Ni nanoparticles on NGDY generated novel hybrid composites, in which Pd-NGDY has high versatility for Suzuki-Miyaura reaction. DFT calculations revealed a charge transfer from NGDY to Pd NPs, and the free energy distribution showed a downward trend for Suzuki-Miyaura coupling reactions.