Aiming at the noise and nonlinear characteristics existing in the deformation monitoring data of concrete dams, this paper proposes a dam deformation prediction model based on a multi-scale adaptive kernel ensemble. The model incorporates Gaussian white noise as a random factor and uses the complete ensemble empirical mode decomposition with adaptive noise (CEEMDAN) method to decompose the data set finely. Each modal component is evaluated by sample entropy (SE) analysis so that the data set can be reconstructed according to the sample entropy value to retain key information. In addition, the model uses partial autocorrelation function (PACF) to determine the correlation between intrinsic modal function (IMF) and historical data. Then, the global search whale optimization algorithm (GSWOA) is used to accurately determine the parameters of kernel extreme learning machine (KELM), which forms the basis of the dam deformation prediction model based on multi-scale adaptive kernel function. The case analysis shows that CEEMDAN-SE-PACF can effectively extract signal features and identify significant components and trends so as to better understand the internal deformation trend of the dam. In terms of algorithm optimization, compared with the WOA algorithm and other algorithms, the results of the GSWOA algorithm are significantly better than other algorithms and have the optimal convergence. In terms of prediction performance, CEEMDAN-SE-PACF-GSWOA-KELM is superior to the CEEMDAN-WOA-KELM, GSWOA-KELM, CEEMDAN-KELM, and KELM models, showing higher accuracy and stronger stability. This improvement is manifested in the decrease of root mean square error (RMSE), mean square error (MSE), and mean absolute error (MAE) and the improvement of the R square (R2) value close to 1. These research results provide a new method for dam safety monitoring and evaluation.