The shallow accretionary prism of the Nankai Trough is a location where both large interplate earthquakes and slow earthquakes occur. Since the physical properties of sedimentary materials are important topics for understanding the structure of the prism, numerous ocean drilling expeditions have been conducted in that region to obtain logging data and core samples. Although the physical properties of the obtained samples are normally measured onboard immediately after coring, estimations of in situ physical properties are difficult because of differences in laboratory and in situ physical conditions. Herein, we propose a new method for estimating in situ porosity from downhole electrical resistivity log data that evaluates in situ porosity and thermal structure simultaneously using correlations between the porosity and resistivity, and between the porosity and thermal conductivity that were established based on laboratory measurements. When constructing physical property correlations, X-ray computed tomography data play an important role in estimating the porosity of samples from which resistivity or thermal conductivity were measured. To validate our method, we compared the estimation with density log data collected at Site C0002 and found that the estimated in situ porosity shows good agreement with the in situ porosity converted from density log data. A comparison with porosity measured onboard for core and cutting samples showed that they are consistent with each other. With this new method, continuous distributions of in situ porosity and thermal structure can be estimated simultaneously based on resistivity log data and heat flow, which are basic quantities acquired during ocean drilling science expeditions. which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.