Accurate sea surface temperature (SST) prediction is of great significance for fishery farming, marine ecological protection, and planning of maritime activities. In this paper, the stacked generalization ensemble is demonstrated for SST prediction to improve every single deep-learning model. Long-term high-resolution satellite-derived SST is used with the sub-regions of the Taiwan Strait and East China Sea taken as the study area. We select the Multilayer Perceptron, Long short-term memory (LSTM), Convolutional Neural Networks (CNN), CNN-LSTM as individual learners, and Convolutional LSTM as the meta-learner. The individual learners are trained and validated on the retained data subset I, while the meta-learner is trained and validated by constructing the samples with the predictions of validated individual learners on the retained data subset II. The two types of models are evaluated on the same test dataset with root-mean-square error and coefficient of efficiency as the scoring criteria. We find that the meta-model outperforms any individual model and other baselines for the one-day-/three-day-ahead forecasts in the Taiwan Strait and one-day-/three-day-/five-day-ahead predictions in the East China Sea. Furthermore, when the lead time is 1 day and 3 days, the meta-model has a better spatial distribution of prediction metrics across all grid points in the Taiwan Strait sub-area. For the East China Sea sub-region, the meta-model advantage is extended to the lead time of 5 days. Probably due to the higher quality of offshore satellite data, the prediction ability enhancement of the stacked ensemble applied in the East China Sea is better than that in the Taiwan Strait. The better-performing meta-model prediction suggests that the stacked generalization ensemble is encouraging and promising for improving the short-term prediction of the daily SST field.