Gold nanorods (GNRs) with longitudinal surface plasmon resonance (LSPR) peaks in second near-infrared (NIR-II) window have attracted a great amount of attention as photothermal transducer because of their inherently excellent photothermal transition efficiency, high biocompatibility and versatile surface functionalization. One key question for the application of these GNRs against tumors in vivo is which size/shape and surface ligand conjugation are promising for circulation and tumor targeting. In this study, we prepared a series of gold nanorods (GNRs) of similar aspect ratio and LSPR peaks, and thus similar photothermal transfer efficiency under irradiation of 980 nm laser, but with tunable size in width and length. The obtained GNRs were subjected to surface modification with PEG and tumor targeting ligand lactoferrin. With these tailor-designed GNRs in hand, we have the chance to study the impact of dimension and surface property of the GNRs on their internalization via tumor cells, photothermal cytotoxicity in vitro, blood circulation and tissue distribution pattern in vivo. As a result, the GNRs with medium size (70 nm in length and 11.5 nm in width) and surface PEG/LF modification (GNR70@PEG-LF) exhibit the fastest cell internalization via HepG2 cells and best photothermal outcome in vitro. The GNR70@PEG-LF also display long circulation time and the highest tumor accumulation in vivo, due to the synergetic effect of surface coating and dimension. Finally, tumor ablation ability of the GNRs under irradiation of 980 nm light were validated on mice xenograft model, suggesting their potential photothermal therapy against cancer in NIR-II window.