Adaptive unscented Kalman filter (AUKF) has been widely used for state of charge (SOC) estimation of lithium-ion battery. The noise covariance of the conventional AUKF method is updated based on the innovation covariance matrix (ICM), which is estimated using the error innovation sequence (EIS). However, the distribution of EIS changes due to the time-varying noise, load current dynamics and modelling error, which will lead to inaccurate ICM estimation. Therefore, an intelligent adaptive unscented Kalman filter (IAUKF) method is proposed to detect the distribution change of EIS. Then, the ICM is estimated based on the EIS after the distribution change. Results show that the IAUKF method can improve SOC estimation accuracy significantly. Compared with that of the AUKF method, the root mean squared error and the mean absolute error of SOC based on the IAUKF method decrease by 43.70% and 72.37% under random walk discharge condition, respectively. In addition, the computation time of the IAUKF method slightly increases by 6.27% compared with that of AUKF method. Finally, the effect of initial parameters on the SOC estimation accuracy was analysed. The results indicate that proper algorithm tuning, such as initial window length of EIS for ICM update and the threshold value, can further improve the SOC accuracy based on the proposed IAUKF method. The proposed IAUKF method also shows high robustness against initial measurement noise covariance.