By analyzing the last 50–60 years of climate changes in Arctic and Subarctic Yakutia, we have identified three distinct periods of climate development. The cold (1965–1987), pre-warming (1988–2004), and modern warming (2005–2023) periods are clearly identifiable. Yakutia’s Arctic and Subarctic regions have experienced mean annual air temperature increases of 2.5 °C and 2.2 °C, respectively, compared to the cold period. The thawing index rose by an average of 171–214 °C-days, while the freezing index dropped by an average of 564–702 °C-days. During the pre-warming period, all three characteristics show a minor increase in warmth. Global warming intensified between 2005 and 2023, resulting in elevated permafrost temperatures and a deeper active layer. Monitoring data from the Tiksi site show that warming has been increasing at different depths since the mid-2000s. As a result, the permafrost temperature increased by 1.7 °C at a depth of 10 m and by 1.1 °C at a depth of 30 m. Soil temperature measurements at meteorological stations and observations at CALM sites both confirm the warming of the permafrost. A permafrost–climatic zoning study was conducted in Arctic and Subarctic Yakutia. Analysis identified seven regions characterized by similar responses to modern global warming. These study results form the foundation for future research on global warming’s effects on permafrost and on how northern Yakutia’s environment and economy adapt to the changing climate.