Displacement prediction models based on measured data have been widely applied in structural health monitoring. However, most models neglect the particularity of displacement monitoring for arch dams with cracks, nor do they thoroughly analyze the non-stationarity and uncertainty of displacement. To address this issue, the influencing factors of displacement were first considered, with crack opening displacement being incorporated into them, leading to the construction of the HSCT model that accounts for the effects of cracks. Feature selection was performed on the factors of the HSCT model utilizing the max-relevance and min-redundancy (mRMR) algorithm, resulting in the screened subset of displacement influence factors. Next, displacement was decomposed into trend, seasonal, and remainder components applying the seasonal-trend decomposition using loess (STL) algorithm. The multifractal characteristics of these displacement components were then analyzed by multifractal detrended fluctuation analysis (MF-DFA). Subsequently, displacement components were predicted employing the convolutional neural network-long short-term memory (CNN-LSTM) model. Finally, the impact of uncertainty factors was quantified using prediction intervals based on the bootstrap method. The results indicate that the proposed methods and models are effective, yielding satisfactory prediction accuracy and providing scientific basis and technical support for the health diagnosis of hydraulic structures.