Accurate estimation of lithium-ion battery capacity is crucial for ensuring its safety and reliability. While data-driven modelling is a common approach for capacity estimation, obtaining cycling data during charging/discharging processes can be challenging. Collecting cycling data under various charging/discharging protocols is often unrealistic, and the collected data can be fragmented due to the random nature of working conditions in practice. To address these issues, we propose a deep transfer learning method that uses partial segments of charging/discharging data for battery capacity estimation. The proposed method utilizes capacity increment features of partial charging/discharging segments that is designed to satisfy practical scenarios. A deep transfer convolutional neural network (DTCNN) is trained with both source and target data, and a fine-tuning strategy is employed to effectively eliminate distribution discrepancies between different battery types or charging/discharging protocols, leading the improved estimation accuracy. Experimental results demonstrate that the proposed method accurately estimates the lithium-ion battery capacity, with values of RMSE, MAPE, and MD-MAPE of only 0.0220, 0.0247, and 0.0194, respectively, when using partial segments. These results highlight the promising prospects of the proposed method for lithium-ion battery capacity estimation.