Research on groundwater recharge has been gradually conducted in Beijing since the South water entered the city in 2014. The land subsidence rate in the region has slowed annually, and some areas have begun to rebound. Owing to new changes in land subsidence in Beijing, it is particularly important to scientifically and reasonably conduct land subsidence prevention and control measurements and accurately identify the water level necessary for prevention and control of land subsidence with its referential meaning. In this study, the critical points of ground subsidence and over-consolidated soil were revealed based on the stratified water level and a long series of subsidence observation data at the ground subsidence monitoring station in Tianzhu. Cross-wavelet and Pearson correlation analyses were performed to quantify the amplitude of the water level and periodic changes in the soil during different periods. The results showed that: \mathrm{①} the over-consolidated soil of the second, third, and fourth aquifers in the study area were -14.30 m, -17.31 m, and -10.12 m, and the water level ranges were 1.73 m, 3.07 m, and 5.03 m, respectively; \mathrm{②} based on the periodic results of the resonance relationship between stratified water level and soil deformation and the peel correlation coefficient, the critical time nodes of land subsidence water level were June, July 2019, and October 2020; and \mathrm{③} the regional stratified storage variables were 97.11×10⁴ m³, 96.57×10⁴ m³, and 92.95×10⁴ m³ by combining the critical water level amplitude change time node and the water level amplitude. The results provide guidance and reference for the prevention and control of land subsidence and groundwater scientific remediation in Beijing and across the entire country.