Abstract: Subsidence induced by groundwater lowering in construction is one of the major risks in the geotechnical engineering currently, which is particularly prominent in Beijing area, whose hydrogeology is characteristized by multi-layered aquifers.In order to predict the problems accurately and conveniently,firstly, based on seepage theory and effective stress principle, the main influencing factors on the compaction of individual layers during groundwater lowering in construction through multi-layered aquifer were analyzed, and the corresponding coupled mathematical model of seepage and compression of subsidence was established. According to the principle of groundwater occurrence and movement, combined with the hydrogeological characteristics of Beijing area, a novel method to determine the bottom boundary of coupled model with major aquifer was proposed, which made the two physical & mechanical processes of seepage and compression coupled under the specific geological conditions, ensured that the that model was scientific and had engineering precision, reduced the difficulty of the actual work of analysis, and improved the practicability of the model analysis. In the aspect of specific storage value of interbed,which was an key paramerter in the model,with hydraulics of groundwater and measured data,the error and its main reason of existing calculation formula was studied, and was combined with the local experience in Beijing area. The correction formula for the specific storage of interbed was introduced, which improved the accuracy of model analysis. Finally, taking a practical project in Beijing area as an example, the detailed simulation of subsidence induced by groundwater lowering in construction through multi-layered aquifer was carried out, and the rationality of the numerical results was analyzed.