The effect of hyperbranched aliphatic polyester (Boltorn series) on the water dissociation in bipolar membranes was firstly investigated in this paper. The bipolar membranes were prepared by immersing the anion exchange layer in a hyperbranched aliphatic polyester solution and then coating on the layer a polyphenylene oxide (SPPO) solution. The SEM observations proved the existence of hyperbranched aliphatic polyester at the membrane intermediate layer. The adsorption amount was evaluated by the oxygen content via XPS. The junction thickness of the prepared bipolar membrane was determined by electrochemical impedance spectroscopy (EIS), and the membrane performances were evaluated by current-voltage curves. The results showed that the amount and generation of Boltorn series, and temperature all affected I-V behaviors of the fabricated bipolar membranes, and the former two played the critical role. These effects were explained on the basis of the water dissociation theory and the characteristics of hyperbranched aliphatic polyester.