The thermal evolution of the permafrost in the sedimentary section of the Tyumen superdeep SG-6 well has been numerically reconstructed using the ICE2020 software package, which is part of the GALO flat basin modeling system. The thermal evolution of the sedimentary strata in the last 3.5 My is considered as the final stage of the basin modeling, whose formation began with continental rifting in the Late Permian. Abrupt climate changes in the late Pliocene–Holocene led to a decrease in the rock temperature by 15–20°C in the upper 1–1.5 km of the SG-6 sedimentary section. The maximum thickness of the permafrost in the study area was about 711 m, reached 2.6 Mya. The maximum thickness of the permafrost for the last ice age (23–18 thous and years ago) was 412 m, reached about 14.5 thousand years ago. According to our modeling, the modern base of the permafrost is at the depth of 311 m and is degrading with the rate about 13 m/1000 y. The results of our calculations with a database of climatic data limited to the last 50 and 100 thousand years differ markedly from the modeling results with the complete database for the last 3.5 My.