Transformation temperatures of authigenic minerals in the diagenetically altered sedimentary rocks of the various basins in Japan were reported. For paleo-temperature analysis, it is necessary to compare the transformation temperatures of authigenic minerals with their actual depth recognized in the well. Various models on the change of paleo-geothermal gradients and the depth variation of authigenic minerals in the sedimentary succession by stratigraphic deficiency were discussed in detail. As an example, paleo-geothermal gradient during Neogene and stratigraphic dificiecy during Quaternary at Nishi-Umaoi SK-3 well drilled in Hokkaido, Japan, were analyzed.