Complex‐shaped nanoparticles as gold nanourchins (GNU) and nanorods (GNR) are very suitable agents in the case of photothermal therapy due to their photon‐heat conversion ability in the red and near‐infrared region (NIR). The quantification in heat generation of complex shaped nanostructures is an important key to predict the therapeutic effect of these nanoparticles. For that, the determination of the nanoparticles absorption cross section (σAbs) responsible for the heat generation is one of the important steps before any application. Although it is obvious to determine σAbs for spheres via Mie's theory, in the case of complex structures like GNU or GNR, this parameter is difficult to model. In this work, a new methodology is used to determine experimentally σAbs for both GNU and GNR. Experimental measurements of the photothermal properties of 100 nm size GNU and two different sizes of GNRs are studied regarding different parameters such as concentration, laser excitation wavelength, and exposure time. By using the heat transfer theory, the temperature elevation in the nanoparticles solutions is converted to temperature elevation at the nanoparticles surface and σAbs values are then calculated for both GNU and GNR in the NIR spectral region.