Nitrogen doped graphdiyne (NGDY) has been reported to have comparable oxygen reduction reaction (ORR) performance to Pt-based catalysts. However, the source of this enhanced ORR performance is not clearly understood. Herein, density functional theory calculations were performed to study the detailed ORR process on NGDY. The theoretically predicted overpotential (η) of GDY materials was 0.442 V, which is comparable to that of Pt-based catalysts, suggesting that GDY is a candidate for non-expensive metal-free ORR catalyst. Our results revealed that the good ORR performance of NGDY originates from the synergy of sp-N and sp2-N, which rules out the experimental proposal that sp-N doping is the dominating factor. Our results further suggest that local positive charge is not a definite descriptor to predict the ORR performance of GDY; instead ΔGO shows a better correlation with performance. Furthermore, it was revealed that the adsorption site is crucial for determining ORR performance, which should not be ignored to fully understand the catalytic activity of GDY-based materials.