Abstract Aiming at the problem of noise and time-delay in temperature prediction modeling of large wave rotor refrigeration process, this paper proposes a novel modeling algorithm that combines the advantages of stacked denoising autoencoder (SDAE) network and Gate Recurrent Unit (GRU) algorithm and utilizes the Maximal Information Coefficient (MIC) algorithm to solve the targeting problem. The MIC algorithm is utilized to calculate the delay time of each input variable and output variable, and the input matrix is reconstructed to compensate for the time-delay, thus solving the problem afterwards. The SDAE network is utilized for denoising the input data and feature extraction to solve the problem of presence of noise in the data. The simulation results show that the proposed MIC-SDAE-GRU algorithm achieves a Root Mean Squared Error (RMSE) of 0.6432 and an R-squared (R²) value of 0.9638, outperforming traditional machine learning methods and other deep learning approaches. Specifically, compared to the standard GRU algorithm, it improves the accuracy of temperature prediction for the wave rotor refrigeration process by 24.7% and exhibits strong generalization ability across various operating conditions.