The endurance of a deep-sea AUV is closely related to its sailing resistance, the amount of carrying batteries and equipment load, which involves interactions among multiple disciplines. In this paper, in order to develop the conceptual design of a long-range AUV in the early stage, a multidisciplinary optimization design framework is presented for decision-makers to explore the given design space, which takes into account the coupling between the disciplines of hull form, structural design and energy use. A Self-adaptive Surrogate Ensemble (SASE) method is proposed to replace the expensive process of hydrodynamic analysis, a recommended approach by the China Classification Society (CCS) specification is applied to carry out the design of metallic pressure hulls, and the classical lamination theory and Tsai–Wu criteria are adopted in the design of composite pressure hulls. Finally, the evaluation model of AUV endurance is created from the perspective of energy capacity and consumption. The conceptual design of a 200 kg-class AUV is executed to maximize the endurance based on the proposed multidisciplinary optimization design framework. The results show that the most important factors that affect AUV endurance are the velocity and diameter, and the optimum velocity of the AUV increases with the load power. The Sea-Whale 2000 AUV was developed based on the optimal result and the excellent endurance performance in the sea trial validated the effectiveness of the proposed design method in the preliminary design process.