As environmental regulations become stricter, the advantages of pure electric vehicles over fuel vehicles are becoming more and more significant. Due to the uncertainty of the actual operating conditions of the vehicle, accurate estimation of the state-of-charge (SOC) of the power battery under multi-temperature scenarios plays an important role in guaranteeing the safety, economy, and reliability of electric vehicles. In this paper, a SOC estimation method based on the fusion of convolutional neural network-transformer (CNN-Transformer) and square root unscented Kalman filter (SRUKF) for lithium-ion batteries in low-temperature scenarios is proposed. First, the CNN-Transformer base model is established. Then, the SRUKF algorithm is used to update the state of the Coulomb counting method results based on the base model results. Finally, ensemble learning theory is applied to estimate SOC in multi-temperature scenarios. Data is obtained from laboratory conditions at −20 °C, −7 °C, and 0 °C. The experimental results show that the SOC estimation method proposed in this study is stable in terms of the root mean square error (RMSE) being between 2.69% and 4.22%. The proposed base model is also compared with the long short-term memory (LSTM) network and gated recurrent unit (GRU) network to demonstrate its relative advantages.