Background <p>The prediction of coronavirus disease in 2019 (COVID-19) in broader regions has been widely researched, but for specific areas such as urban areas the predictive models were rarely studied. It may be inaccurate to apply predictive models from a broad region directly to a small area. This paper builds a prediction approach for small size COVID-19 time series in a city.</p> Methods <p>Numbers of COVID-19 daily confirmed cases were collected from November 1, 2022 to November 16, 2023 in Xuzhou city of China. Classical deep learning models including recurrent neural network (RNN), long and short-term memory (LSTM), gated recurrent unit (GRU) and temporal convolutional network (TCN) are initially trained, then RNN, LSTM and GRU are integrated with a new attention mechanism and transfer learning to improve the performance. Ten times ablation experiments are conducted to show the robustness of the performance in prediction. The performances among the models are compared by the mean absolute error, root mean square error and coefficient of determination.</p> Results <p>LSTM outperforms than others, and TCN has the worst generalization ability. Thus, LSTM is integrated with the new attention mechanism to construct an LSTMATT model, which improves the performance. LSTMATT is trained on the smoothed time series curve through frequency domain convolution augmentation, then transfer learning is adopted to transfer the learned features back to the original time series resulting in a TLLA model that further improves the performance. RNN and GRU are also integrated with the attention mechanism and transfer learning and their performances are also improved, but TLLA still performs best.</p> Conclusions <p>The TLLA model has the best prediction performance for the time series of COVID-19 daily confirmed cases, and the new attention mechanism and transfer learning contribute to improve the prediction performance in the flatten part and the jagged part, respectively.</p>