Autonomous underwater vehicles (AUVs) have the characteristics of a high performance, a complex coupling mechanism, a compact, complex system composition, as well as high requirements for design constraints, quality, and reliability. In the traditional overall design process, numerous design tools and software programs are used, which results in poor model data sharing, a lack of uniqueness and synchronization between system levels, and difficulty in process tracing. Moreover, it is challenging to meet the technical requirements for close collaboration and rapid iteration of multiple positions. To address the aforementioned limitations, this study proposes a digital overall integrated design method for the design and simulation integration of AUVs and defines a unified architecture and interface for system-level design simulation models, thus solving the interoperability and consistency problems in multiple tools and models. In addition, a model-based AUV system integration design verification method that combines different processes, specifications, and models is designed, and software similar to Cameo, which can provide technical means for system-level integrated design and achieve rapid modeling and simulation verification based on system design solutions, is developed. Finally, a practical system design is conducted by taking specific AUV equipment as a research object, and the proposed methods are compared with traditional methods to prove the improvement effect of the technical route on the equipment and development efficiency.