Subsidence of a foundation caused by liquefaction of sandy soil is a critical step in the creation of a building. Seven measured indicators of soil liquefaction in the course of an earthquake were selected as key impacting indicators that predict subsidence of a building. These indicators are the earthquake intensity EI, length-height ratio L/H, average contact pressure p, width-depth ratio, relative density D-R, thickness of the non-liquefied layer, and the depth of the gravel layer. Furthermore, as a probabilistic machine learning kernel and powerful tool for solving highly nonlinear problems, Gaussian process regression (GPR model) can meet execution time requirements and assure a high level of precision of subsidence prediction due to the intrinsic defects of theoretical analysis and numerical calculation. A total of 41 groups of typical cases were first selected as a training sample and 20 groups of typical cases were defined as a test sample, where these cases possess input test value and were obtained at the yield of the prediction accuracy from the GPR model. Next, the PLS method, MLR method and LSSVM method were selected to verify the validity and reliability of the GPR model. Finally, the simulation result shows that the GPR model can improve the prediction precision for the case of the above problems and is of great value for practical applications.