This study addresses the challenges of predicting ship heave motion in real time, which is essential for mitigating sensor–actuator delays in high-performance active compensation control. Traditional methods often fall short due to training on specific sea conditions, and they lack real-time prediction capabilities. To overcome these limitations, this study introduces a multi-step prediction model based on a Seq2Seq framework, training with heave data taken from various sea conditions. The model features a long-term encoder with attention-enhanced Bi-LSTM, a short-term encoder with Gated CNN, and a decoder composed of multiple fully connected layers. The long-term encoder and short-term encoder are designed to maximize the extraction of global characteristics and multi-scale short-term features of heave data, respectively. An optimized Huber loss function is used to improve the fitting performance in peak and valley regions. The experimental results demonstrate that this model outperforms baseline methods across all metrics, providing precise predictions for high-sampling-rate real-time applications. Trained on simulated sea conditions and fine-tuned through transfer learning on actual ship data, the proposed model shows strong generalization with prediction errors smaller than 0.02 m. Based on both results from the regular test and the generalization test, the model’s predictive performance is shown to meet the necessary criteria for active heave compensation control.