Controlling the localized heat generation density and temperature profile of nanostructures exploiting perfect absorption of individual resonance modes is reported. The methodology is applied to spherically symmetric nanostructures using the T-matrix method. It is demonstrated that perfect modal splitting of the absorption power at desired wavelengths and individual excitation of the modes provide the ability to localize the generated heat at desired locations, and control the resulting temperature profile in multilayer core–shell structures. By knowing the thermal behavior of individual modes, it is shown that excitation of the perfect absorption modes at desired temperatures can result in compensation for the temperature-rise drop, induced in high-temperature thermoplasmonics due to thermal shift of the resonance frequencies. Much higher temperature rises can be achieved through properly designed thermal mode-coupling schemes. The proposed methodology is very promising for the control of the thermoplasmonic behavior of nanostructures, and the design of much more thermally efficient structures, taking into account the thermally dependent parameters.