Three diketopyrrolopyrrole-based photosensitizers (S1, Se1 and Se2) were designed to optimize the contributions of photodynamic (PDT) and photothermal (PTT) therapy in tumor phototherapy via adjusting the spin-orbit coupling constant and the intersystem crossing efficacy. The photo-physicochemical as well as biological properties indicated that the introduction of Se and methoxy group can increase the ISC rate of the photosensitizers with increased PDT efficiency and decreased PTT effects, which were in accordance with the results of DFT and TD-DFT calculations. Importantly, the in vivo evaluations revealed that supramolecular nanoparticles Se2-NPs showed excellent phototherapeutic performance via synergistic PDT and PTT against cancer. These findings suggest that controlling the relative contributions of PDT and PTT may be an effective way to improve phototherapy efficiency.