The present work summarizes the results of analysis of unique experimental data on vertical heat flow variations in different geological structures obtained from 15 scientific supper-deep and deep boreholes drilled to the depths of 1600-12 262 m within Russian and ICDP programs. The new workflow was applied for the heat flow estimation which is based on (1) precise and detailed thermal conductivity measurements on more than 30 000 cores with the new emerging technologies, (2) usage of more than 100 equilibrium and non-equilibrium temperature logs, and (3) determination of conductive heat flow component within 20-100 m intervals along every borehole studied. The data on conductive heat flow variations provides an estimate of vertical variations in the convective heat flow component. The latter reflects the information on variations in reservoir and formation properties and heat- and mass transfer processes in reservoirs and formations. It was established that a conductive component of the heat flow varies between 70 and 100% for the boreholes studied with essential (up to 100%) increase in heat flow within upper depth intervals of 2-4 km in some cases. Terrestrial heat flow values established from the measurements in deep and super-deep boreholes exceed the previous experimental heat flow estimates by 30...130% depending on a region of drilling. During the previous estimates the heat flow values were obtained from the measurements in shallow boreholes and heat flow was determined from averaging temperature gradient and thermal conductivity along boreholes. The established heat flow variations play an important role in the improvement of reliability of basin and petroleum system modeling and prediction of temperatures below the borehole depths. The use of calibrated heat flow distributions is shown to increase the confidence of such studies.