By applying nonequilibrium Green’s functions in combination with the density-functional theory, we investigate the electronic, thermal, and thermoelectric properties of four kinds of bases in DNA perpendicularly coupling between two ZGNR electrodes. The results show that the electron transport is highly sensitive to different base-ZGNR coupling geometries, and the system can present large rectifying and negative differential resistance effects. Moreover, the fluctuations of electronic transmission and super-low thermal conductance result in significant enhancement of the thermoelectric figure of merit (ZT): the ZT will be over 1.4 at room temperature, and over 1.6 at 200 K. The results show that the base-ZGNR coupling devices can present large rectifying, negative differential resistance, and enhanced thermoelectric effects.