For super-tall buildings, temperature is one of the most significant factors to affect the structural response. However, very few studies have been conducted on the temperature effects of the super-tall buildings due to their large size and complicated configuration. A long-term structural health monitoring (SHM) system consisting of over 800 sensors of 16 types has been implemented on Canton Tower, a tube-in-tube super-tall structure for real-time monitoring at both construction and service stages. As one part of this sophisticated SHM system, 48 and 96 temperature sensors have been deployed at 12 cross-sections of the inner and outer tubes, respectively. The real-time temperature at each measurement point could be collected through this system, but it's still difficult to obtain the temperature distribution of the whole tower with limited measurement points. In this paper, the FE model of a typical section for inner tube and one for the column of the outer tube are constructed to investigate the temperature distribution through the heat transfer analysis. To verify the effectiveness of the model, the simulated results are compared with the field monitoring data. The simulated results show a good agreement with the measurements. The temperature distribution can be obtained by integrating the simulated and measured results and served as an input into the FE model of Canton Tower to calculate the temperature-induced deformation and force.