This study developed a transformer-based deep learning model to predict the Arctic sea ice seasonally. By integrating the sea ice thickness data into the model, the spring prediction barrier of Arctic sea ice is optimized significantly. The model achieves better skills than the typical numerical model in predicting September’s sea ice extent seasonally. The sea ice thickness data play a key role in reducing the prediction errors of the Beaufort Sea, the East Siberian Sea and the Laptev Sea.