Gold nanorods (AuNRs) have shown great potential as photothermal agents for cancer therapy. However, the biosafety of AuNRs ordinarily synthesized using a cationic ligand assistance procedure has always been a subject of controversy, which limits their application in tumor therapy. In this study, we propose a novel strategy to enhance the biocompatibility of AuNRs by constructing a biological coating derived from silk fibroin (SF) on their surface. The SF coating could be easily and precisely manipulated using a layer-by-layer (LBL) assembly method. The resulting SF-coated gold nanorods (AuNRs@SF) exhibited reduced cytotoxicity and improved hemocompatibility compared to untreated AuNRs. Moreover, the treated nanorods were easily modified with a tumor-targeting peptide (AuNRs@MTSF) and efficiently loaded indocyanine green (ICG). Both in vitro and in vivo analyses demonstrated that AuNRs@MTSF could more effectively reach tumor tissue and enter MCF-7 cells. Furthermore, after loading ICG, AuNRs@MTSF exhibited superior antitumor efficacy compared to other groups by combining photodynamic therapy (PDT) with photothermal therapy (PTT) under near-infrared (NIR) irradiation without inducing any side effects. This work suggests that SF coating of gold nanorods is a potential approach for improving their biocompatibility, and that function-modified AuNRs@SF are effective nanoplatforms for targeted and multimodal tumor therapy.