During a microwave hyperthermia oncology treatment, the target region temperature is elevated to the temperatures of 40–44 °C, which improves the therapeutic effect of a standard radiotherapy and/or chemotherapy treatments. Amplitudes and phases of antenna input signals in the phased array setup surrounding the 3D patient model are optimised with respect to maximise the energy deposition in the target region. In this study, we successfully integrated an automatic artificial intelligence segmentation routine, used for patient-specific 3D model generation, into the hyperthermia treatment planning process. This allows us to apply more realistic patient 3D model for the online hyperthermia guidance including detailed retrospective analyses of the overall treatment quality, possibly leading to a widespread clinical use of the hyperthermia treatment planning.