It remains challenging to develop an effective therapeutic agent for breast cancer. Synergistic therapies, particularly chemo-photothermal therapy, have gained increasing attention in cancer treatment. While the high working temperature achieved in photothermal therapy can kill tumor cells, it also causes thermal damage to nearby healthy cells, limiting the clinical application of chemo-photothermal synergistic therapy. To address these limitations, we have successfully synthesized nanoparticles by combining mesoporous polydopamine with atovaquone (ATO), denoted MPDA-ATO. These nanoparticles (NPs) enable chemophotothermal therapy to be conducted at a mildly increased temperature of 46 °C. The MPDA-ATO NPs exhibit excellent photothermal stability, potent photothermal conversion properties, and good biocompatibility. In response to near-infrared radiation (NIR), MPDA-ATO can effectively kill 4T1 breast tumor cells in vitro and in the synergistic host. Furthermore, the MPDA-ATO NPs specifically inhibit STAT3, contributing to the antitumor effect. The treatment combining MPDA-ATO NPs with NIR could induce the apoptosis of tumor cells. In summary, the MPDA-ATO NPs offer improved efficacy and safety in treating breast cancer, providing insights and strategies for improved breast cancer therapy.