A core-shell composite consisting of polypyrrole (PPy) coating on Au nanorods with high two-photon photothermal efficiency and good photostability have been fabricated via a facile interfacial polymerization. Transmission electron microscopy confirmed the core-shell structure of the uniform Au-PPy nanorods. The core-shell composites exhibited improved temperature elevation and photostability compared to pure Au nanorods. The composites internalized by cancer cells can be detected by strong two-photon fluorescence, thus minimizing photothermal damage to normal tissues. The cell cytotoxicity and two-photon efficiency experiments in vitro demonstrate that the composites of Au-PPy nanorods have high efficiency to inhibit the proliferation of tumor cells.