The prediction of land subsidence is of significant value for the early warning and prevention of geological disasters. Although numerous land subsidence prediction methods are currently available, two obstacles still exist: (i) spatio-temporal heterogeneity of land subsidence is not well considered, and (ii) the prediction performance of individual models is unsatisfactory when the data do not meet their assumptions. To address these issues, we developed a spatio-temporal heterogeneous ensemble learning method for predicting land subsidence. Firstly, a two-stage hybrid spatio-temporal clustering method was proposed to divide the dataset into internally homogeneous spatio-temporal clusters. Secondly, within each spatio-temporal cluster, an ensemble learning strategy was employed to combine one time series prediction model and three spatio-temporal prediction models to reduce the prediction uncertainty of an individual model. Experiments on a land subsidence dataset from Cangzhou, China, show that the prediction accuracy of the proposed method is significantly higher than that of four individual prediction models.