The long-term over-exploitation of groundwater has not only caused the compaction of aquifer thickness and surface deformation but has also further aggravated the loss of groundwater storage (GWS) in Beijing plain. The South-to-North Water Diversion Project (SNWDP) furnishes a new source of water for Beijing. By reviewing related studies, it was found that there are few studies on the realization of GWS estimation based on InSAR technology considering the lag effect. Therefore, in this study, firstly, the long-time series deformation characteristics of Beijing plain were obtained from 46 RadarSat-2 images using small baseline subset interferometric synthetic aperture radar (SBAS-InSAR) technology. Secondly, the seasonal components of surface deformation and hydraulic head change were extracted by means of multichannel singular spectrum analysis (MSSA), verifying the separation accuracy by means of Monto Carlo-SSA (MC-SSA). Finally, for the hydrodynamic delay (aquifer water supply/drainage) of the complex aquifer system, we introduced the time lag cross-correlation (TLCC) approach to correct the hysteresis response of seasonal deformation relative to the variation of the aquifer system head, so as to realize the estimation of aquifer storage properties and GWS loss, even unrecoverable GWS (UGWS). The results showed that the average annual variation of total GWS (TGWS) in Beijing plain was −6.702 × 10⁷ m³, of which the depletion volume of UGWS was −6.168 × 10⁷ m³, accounting for 92.03% of the TGWS. On a temporal scale, the depletion of UGWS lagged behind the total head change, with about one year of lag time. On a spatial scale, in contrast to the north of Beijing plain, the depletion of UGWS in the south only recovered briefly after 2015 and then continued to decline. This further indicated that the process of the decline of middle-deep confined head and long-term GWS loss caused by over-exploitation of groundwater was irreversible. These findings are of great significance to optimize the allocation of groundwater resources, reduce the harm of land subsidence and protect groundwater resources.