The friction behaviour of ZnO nanowires on natural graphite (NG) and highly oriented pyrolytic graphite (HOPG) substrates was tested in ambient conditions by use of optical microscopy based nanomanipulation. Nanowires on the step-free and waviness-free NG substrate exhibit a diameter-independent nominal frictional shear stress of 0.48 MPa, and this provides a benchmark for studying how the surface topography of graphite influences nanowire friction. Nanowires on the HOPG substrate present a significant diameter-dependent frictional shear stress, increasing from 0.25 to 2.78 MPa with the decrease of nanowire diameter from 485 to 142 nm. The waviness of HOPG has a limited effect on the nanowire friction, as a nanowire can fully conform to the substrate. The surface steps on the HOPG can significantly enhance the nanowire friction and lead to a much higher frictional shear stress than that on NG due to mechanical blocking and the presence of a Schwoebel barrier at step edges. The surface steps, however, can also generate small wedge-shaped gaps between a nanowire and substrate, and thus reduce the nanowire friction. With the decrease in nanowire diameter, the capacity for the nanowire to better conform to the substrate reduces the length of the wedge-shaped gaps, leading to the observed increase in nanowire friction. The results have improved our understanding of the unique friction behaviour of nanowires. Such an improved understanding is expected to benefit the design and operation of nanowire-friction-based devices, including bio-inspired fibrillar adhesives, soft grippers, rotary nanomotors, and triboelectric nanogenerators.