Photothermal therapy (PTT) is a promising alternative therapy for benign or even malignant tumors. To improve the selective heating of tumor cells, target-specific photothermal conversion agents are often included, especially nanoparticles. Meanwhile, some indirect methods by manipulating the radiation and heat delivery are also adopted. Therefore, to gain a clear understanding of the mechanism, and to improve the controllability of PTT, a few issues need to be clarified, including bioheat and radiation transfer, localized and collective heating of nanoparticles, etc. In this review, we provide an introduction to the typical bioheat transfer and radiation transfer models along with the dynamic thermophysical properties of biological tissue. On this basis, we reviewed the most recent advances in the temperature control methods in PTT from macroscale to nanoscale. Most importantly, a comprehensive introduction of the localized and collective heating effects of nanoparticle clusters is provided to give a clear insight into the mechanism for PPT from the microscale and nanoscale point of view.