Malignant bone tumors have a high mortality rate and usually occur in adolescents. Postoperative chemotherapy often cannot completely eliminate the tumor tissue, and bone regeneration is complex when bone tumors cause large bone defects. Additionally, the local and systemic toxicity caused by chemotherapy can affect the bone repair and living quality of patient. Therefore, striking a balance between tumor therapy and toxicity is a critical component of anti-tumor research. Photothermal therapy (PTT) has aroused the interest of researchers based on its potential to balance the effects of near-infrared (NIR)-based PTT and toxicity in tumor therapy. The advantages of NIR-triggered PTT include the ability to penetrate tumor tissue, decreased local and systemic damage, and ease of control. This review focuses on applying bone repair biomaterials with photothermal effects in treating large bone defects caused by bone tumors. Specifically, the balance between toxicity, photothermal effect, and promotion of osteogenesis is discussed for different scaffolds. This provides reference information for developing a new generation of biomaterials for treating malignant bone tumors.