To explore the potential of silicon quantum dots (SiQDs) in combined photodynamic therapy (PDT) and photothermal therapy (PTT), we engineered the surface of SiQDs with the photosensitizer Ce6 and the tumor-cell-targeting ligand phenylboronic acid (PBA) via polydopamine-mediated chemistry. Upon irradiation with light of specific wavelengths, SiQDs@Ce6/PBA could generate high levels of reactive oxygen species (ROS) and trigger effective photo-to-thermal conversion. PBA-conjugation could not only increase the cellular uptake and transcellular transport capability of nanoparticles, but also enhance their tumor accumulation. In the presence of a 635 nm laser, SiQDs@Ce6/PBA was able to trigger intracellular ROS production, which further altered the mitochondrial membrane potential and promoted apoptosis of tumor cells. Finally, combined PDT/PTT treatments led to synergistically enhanced cancer cell killing and tumor-growth inhibition effects. This study demonstrates the surface engineering of silicon quantum dots for synergistic PDT/PTT cancer therapy.