Aiming at the problem that the existing battery fractional order model is not suitable for the auxiliary power battery of hydrogen fuel cell heavy-duty trucks, considering the characteristics of multiple influencing factors and nonlinearity in actual driving processes, a fractional order model of auxiliary power batteries is proposed based on the hydrogen fuel cell heavy-duty trucks model and the batteries' fractional order model. Then, to solve the charge state estimation error increases due to the high frequency and large rate charging and discharging, H∞ filter is introduced into the adaptive unscented Kalman filter to optimize the charge state estimation in the model. Additionally, the model's parameters are identified using the evolutionary algorithm and the recursive least squares technique based on the forgetting factor. Finally, the model is verified by dynamic conditions. The results show that compared with the auxiliary power batteries' fractional order model, the optimized model reduces the MAE by 0.08% and the RMSE by 0.22% when estimating voltage, and reduces the MAE by 0.25% and the RMSE by 2.66% when estimating SOC. Therefore, the optimized fractional order model of auxiliary power battery has higher accuracy and applicability.