Abstract Accurately estimating the state of health (SOH) of lithium-ion batteries is important for improving battery safety performance. The single time-domain feature extraction is hard to efficiently extract discriminative features from strongly nonlinear coupled data, leading to difficulties in accurately estimating the battery SOH. To this end, this paper proposes a multi-scale frequency domain feature and time domain feature fusion method for SOH estimation of lithium-ion batteries based on the Transformer model. Firstly, the voltage, current, temperature and time information of the battery are extracted as time domain features; secondly, the battery signal is processed by a multi-scale filter bank based on Mel-frequency cepstral coefficients (MFCC) to obtain the multi-scale frequency domain features; then, a parallel focusing network (PFN) is designed to fuse the time domain features with the frequency domain features, which yields low-coupling complementary discriminative features; finally, constructing the SOH estimation mechanism based on the Transformer deep network model. The algorithm is validated by NASA and Oxford datasets, the mean's absolute error (MAE) and root mean square error (RMSE) are as low as 0.06% and 0.23%, respectively.