Battery has been widely used in the storage of new energy. In this paper, we focus on the research of the controller design of a battery charging system, in which an isolated dual converter is used for energy conversion. In practical applications, the performance of the battery charging system is always affected by the uncertain circuit parameters. In order to improve its dynamic and steady performance under various uncertainties, a sliding mode control (SMC) strategy is proposed in this paper for the control of the battery charging system. First, the working principle of the isolated dual converter with parameter uncertainties is analyzed in this paper. Then, based on the model of the battery charging system, a SMC strategy based on the Pulse Width Modulation (PWM) method is designed and analyzed in this paper. The influence of variation of switching frequency on the controller parameters design is also discussed in this paper. Finally, simulation results show that, compared with the existing method, the control strategy proposed in this paper is robust to the system parameter uncertainties and the close loop battery charging system has better transient and steady performance.