Structural monitoring is crucial for assessing structural health, and high-precision deformation prediction can provide early warnings for safety monitoring. To address the issue of low prediction accuracy caused by the non-stationary and nonlinear characteristics of deformation sequences, this paper proposes a similarity clustering (SC) deformation prediction model based on GNSS/accelerometer time-frequency analysis. First, the complete ensemble empirical mode decomposition with adaptive noise (CEEMDAN) algorithm is used to decompose the original monitoring data, and the time-frequency characteristic correlations of the deformation data are established. Then, similarity clustering is conducted for the monitoring sub-sequences based on their frequency domain characteristics, and clustered sequences are combined subsequently. Finally, the Long Short-Term Memory (LSTM) model is used to separately predict GNSS displacement and acceleration with clustered time series, and the overall deformation displacement is reconstructed based on the predicted GNSS displacement and acceleration-derived displacement. A shake table simulation experiment was conducted to validate the feasibility and performance of the proposed CEEMDAN-SC-LSTM model. A duration of 5 s displacement prediction is analyzed after 153 s of monitoring data training. The results demonstrate that the root mean square error (RMSE) of predicted displacement is 0.011 m with the proposed model, which achieves an improvement of 64.45% and 61.51% in comparison to the CEEMDAN-LSTM and LSTM models, respectively. The acceleration predictions also show an improvement of 96.49% and 95.58%, respectively, the RMSE of the predicted acceleration-reconstructed displacement is less than 1 mm, with a reconstruction similarity of over 99%. The overall displacement reconstruction similarity can reach over 95%.