The file “GCOS_EHI_1960-2020_Continental_Heat_Content_data.nc” presents an updated estimate of the global continental heat storage for the period 1960-2020. For the first time, the continental heat storage is assessed as composed by: ground heat storage due to changes in subsurface temperatures, inland water heat storage due to the warming of inland water bodies, and permafrost heat storage due to thawing of ground ice in the Arctic. Furthermore, we argue that all three components of the continental heat storage should be monitored independently of their relative magnitude, as heat gain in the three components alters several important climate phenomena affecting society and ecosystems. This file contains the total continental heat storage relative to 1960. The ground heat storage has been estimated by inverting 1079 subsurface temperature profiles form the Xibalbá database (https://figshare.com/articles/dataset/Xibalb_Underground_Temperature_Database/13516487) and a bootstrap technique to aggregate the Singular Value Decomposition (SVD) inversions of each profile (Cuesta-Valero et al., 2022a). The data are used in Cuesta-Valero et al. (2022b) and von Schuckmann et al. (2022).