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By applying nonequilibrium Green’s function in combination with the density-functional theory, we investigate the electronic transport properties of boron or nitrogen doped zigzag phagraphene nanoribbon junctions. Our calculated results show that the negative differential resistance effect could be observed in zigzag phagraphene nanoribbon junction. Moreover, the peak to valley ratio of the negative differential resistance significantly increase from 1.6 to 111.32, when the junction is doped by boron atoms. We rationalize the mechanism leading to negative differential resistance by providing a detailed analysis of transmission spectra and transmission pathways.