The application of photothermal therapy (PTT) to defeat bacterial infections has attracted great attention in the past years. Prussian blue (PB) is a potential photothermal agent in bacteria obliteration. The electron density of cyanide bonds (CN) in PB plays a decisive role on its PTT performance. Meanwhile, recent reports indicated that encapsulating PB shell on lanthanide nanomaterials core could effectively enhance its photothermal efficiency. Hence, a series of lanthanide ions, including erbium (Er3+), dysprosium (Dy3+), thulium (Tm3+), ytterbium (Yb3+), doped PB nanocubes were fabricated by a simple doping method due to the differences between lanthanide and iron on changing electron density of cyanide bond. And the Yb3+ doped PB (PB-Yb) has the best PTT performance of all nanocubes. Structure analyzing results indicate that 9% Fe (Fe2+ or Fe3+) were replaced by Yb3+ in PB-Yb, which could raise its electron density to improve its PTT performance. And the antibacterial test also verified the conclusion. All above results proved that doping proper lanthanide ions into PB is a simple and effective way to improve its photothermal performance.