By using nonequilibrium Green's functions in combination with the density-functional theory, we investigate the effects of B and N doping on the transport properties in phenalenyl molecular device. The calculated results show that negative differential resistance behavior can be observed in phenalenyl molecular device where the device current can decrease with the base voltage increasing particularly in a bias voltage region, and the peak-to-valley current ratio reaches up to 5.12. The device current can be increased before 0.8 V when the molecular center atom is replaced by B or N atom. But, the negative differential resistance behavior can be weakened and the peak-to-valley current ratio can decrease to 3.83 and 3.61, respectively. The doping effects of B and N, which are induced by the difference in extranuclear electron number between them, can make the orbitals and corresponding transmission peaks move toward high or low energy to modulate the electronic transport ability and the negative differential resistance behavior of the device.