The freeze–thaw (F-T) cycle of the active layer (AL) causes the “frost heave and thaw settlement” deformation of the terrain surface. Accurately identifying its amplitude and time characteristics is important for climate, hydrology, and ecology research in permafrost regions. We used Sentinel-1 SAR data and small baseline subset-interferometric synthetic aperture radar (SBAS-InSAR) technology to obtain the characteristics of F-T cycles in the Zonag Lake-Yanhu Lake permafrost-affected endorheic basin on the Qinghai-Tibet Plateau from 2017 to 2019. The results show that the seasonal deformation amplitude (SDA) in the study area mainly ranges from 0 to 60 mm, with an average value of 19 mm. The date of maximum frost heave (MFH) occurred between November 27th and March 21st of the following year, averaged in date of the year (DOY) 37. The maximum thaw settlement (MTS) occurred between July 25th and September 21st, averaged in DOY 225. The thawing duration is the thawing process lasting about 193 days. The spatial distribution differences in SDA, the date of MFH, and the date of MTS are relatively significant, but there is no apparent spatial difference in thawing duration. Although the SDA in the study area is mainly affected by the thermal state of permafrost, it still has the most apparent relationship with vegetation cover, the soil water content in AL, and active layer thickness. SDA has an apparent negative and positive correlation with the date of MFH and the date of MTS. In addition, due to the influence of soil texture and seasonal rivers, the seasonal deformation characteristics of the alluvial-diluvial area are different from those of the surrounding areas. This study provides a method for analyzing the F-T cycle of the AL using multi-temporal InSAR technology.