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Some important discoveries have been revealed in some studies, including that the settlement of concrete face rockfill dams (CFRDs) may cause cracks in the concrete face slabs, which may lead to dam collapse. Therefore, deformation behavior prediction of CFRDs is a longstanding and emerging aspect of dam safety monitoring. This paper aims to propose a settlement prediction model for CFRDs combining the variational mode decomposition (VMD) algorithm, long short-term memory (LSTM) network, and support vector regression algorithm (SVR). Firstly, VMD is applied in the decomposition of dam settlement monitoring data to reduce its complexity. Furthermore, feature information on settlement time series is extracted. Secondly, the LSTM and SVR are optimized by the Harris hawks optimization (HHO) algorithm and modified least square (PLS) method to mine the major influencing factors and establish the prediction model with higher precision. Finally, the proposed model and other models are applied to predict the deformation behavior of the Yixing CFRD. Prediction results indicate that the proposed method possesses particular advantages over other models. The proposed VMD-LSTM-SVR model might help to evaluate the settlement trends and safety states of CFRDs.